[R] Compare species presence and absence between sites

[Rui Barradas]

Hello,

Maybe something like the following.

res <- different(mat["B",], mat["E",])
res[res]


Rui Barradas

Em 27-09-2013 23:11, Elaine Kuo escreveu:
> Thanks Rui and Arun.
> Both worked well.
>
> One more question, what shall I add for Rui's code if only the comparison
> of TRUE (no FALSE) to be shown in the result?
>
> Elaine
>
> code
> different <- function(x, y) x == 1 & y == 0
>
> set.seed(7054)
> mat <- matrix(sample(0:1, 500, TRUE), nrow = 5)
> rownames(mat) <- LETTERS[1:5]
> colnames(mat) <- sprintf("D%03d", 1:100)
>
> different(mat["B",], mat["E",])
>
>
> On Fri, Sep 27, 2013 at 9:31 PM, arun <smartpink111 at yahoo.com> wrote:
>
>> Just to add:
>>
>> If you wanted the difference of every combination of rows:
>> set.seed(248)
>>   mat1<-
>> matrix(sample(0:1,5*100,replace=TRUE),ncol=100,dimnames=list(LETTERS[1:5],paste0("D",sprintf("%03d",1:100)))
>> )
>>   dat<-expand.grid(LETTERS[1:5],LETTERS[1:5],stringsAsFactors=FALSE)
>> dat1<-dat[!paste0(dat[,1],dat[,2]) %in% paste0(LETTERS[1:5],LETTERS[1:5]),]
>>   lst1<- lapply(seq_len(nrow(dat1)),function(i)
>> {x<-mat1[unlist(dat1[i,]),]; which(different(x[1,],x[2,]))}) #using Rui's
>> function
>> names(lst1)<- paste(dat1[,1],dat1[,2],sep="_")
>>
>>
>> A.K.
>>
>>
>>
>> ----- Original Message -----
>> From: Rui Barradas <ruipbarradas at sapo.pt>
>> To: Elaine Kuo <elaine.kuo.tw at gmail.com>
>> Cc: "r-help at r-project.org" <r-help at r-project.org>
>> Sent: Friday, September 27, 2013 7:39 AM
>> Subject: Re: [R] Compare species presence and absence between sites
>>
>> Hello,
>>
>> Something like this?
>>
>>
>> different <- function(x, y) x == 1 & y == 0
>>
>> set.seed(7054)
>> mat <- matrix(sample(0:1, 500, TRUE), nrow = 5)
>> rownames(mat) <- LETTERS[1:5]
>> colnames(mat) <- sprintf("D%03d", 1:100)
>>
>> different(mat["B",], mat["E",])
>>
>>
>>
>> Hope this helps,
>>
>> Rui Barradas
>>
>> Em 27-09-2013 11:48, Elaine Kuo escreveu:
>>> Dear List,
>>>
>>>
>>>
>>> I want to compare the presence and absence of bird species based on the
>>> sites in a matrix.
>>>
>>> The matrix has 5 rows for Island A, B, C, D, and E.
>>>
>>> It has 100 columns for bird species D001-D100.
>>>
>>> In each cell of the matrix,
>>>
>>> the presence-absence of bird species will be recorded as 1 or 0.
>>>
>>> (For example, if species D001 is found on Island D,
>>>
>>> the matrix cell of species D001 and Island D will be 1.)
>>>
>>>
>>>
>>> Now I want to know the different bird species between Island B and E.
>>>
>>> In other words, I would like to find out bird species present (1) on
>> Island
>>> B but absent (0)on island E, and vice versa (absent (0) on Island B but
>>> present (1)on island E).
>>>
>>>
>>>
>>> Please kindly advise how to code the purpose above.
>>>
>>> Thank you in advance.
>>>
>>>
>>>
>>> Elaine
>>>
>>>      [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-help at r-project.org 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 at r-project.org 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.
>>
>>
>