[R] matrix help (first occurrence of variable in column)

[Michael Denslow]

On Wed, May 18, 2011 at 9:49 PM, jim holtman <jholtman at gmail.com> wrote:
> Is this what you were after:
>
>> mdat <- matrix(c(1,0,1,1,1,0), nrow = 2, ncol=3, byrow=TRUE,
> +               dimnames = list(c("T1", "T2"),
> +                               c("sp.1", "sp.2", "sp.3")))
>>
>> mdat
>   sp.1 sp.2 sp.3
> T1    1    0    1
> T2    1    1    0
>> # do 'rle' on each column and see if it is length >1 and starts with zero
>> mdat.df <- as.data.frame(mdat)
>> new.spec <- sapply(mdat.df, function(x){
> +     x.rle <- rle(x)
> +     (length(x.rle$values) > 1) & (x.rle$values[1L] == 0)
> + })
>> names(mdat.df)[new.spec]
> [1] "sp.2"
>>

Thanks for your reply!
This is close to what I want, but I think it only works if there is
two rows. My actual data could have up to 8 rows (time samples).

An example with 4 rows:

mdat3 <- matrix(c(1,0,0,1,0,1,0,0,1,0,1,1,1,0,0,1,0,1,1,1), nrow = 4,
ncol=5, byrow=TRUE,
               dimnames = list(c("T1", "T2",'T3','T4'),
                               c("sp.1", "sp.2", "sp.3","sp.4","sp.5")))

mdat3

mdat.df <- as.data.frame(mdat3)
new.spec <- sapply(mdat.df, function(x){
    x.rle <- rle(x)
    (length(x.rle$values) > 1) & (x.rle$values[1L] == 0)
	})

names(mdat.df)[new.spec]

It should say sp.5 since all the other species have occurred in other
samples. Any further help would be much appreciated.


>
> On Wed, May 18, 2011 at 9:37 AM, Michael Denslow
> <michael.denslow at gmail.com> wrote:
>> Dear R help,
>> Apologies for the less than informative subject line. I will do my
>> best to describe my problem.
>>
>> Consider the following matrix:
>>
>> mdat <- matrix(c(1,0,1,1,1,0), nrow = 2, ncol=3, byrow=TRUE,
>>               dimnames = list(c("T1", "T2"),
>>                               c("sp.1", "sp.2", "sp.3")))
>>
>> mdat
>>
>> In my actual data I have time (rows) and species occurrences (0/1
>> values, columns). I want to count the number of new species that occur
>> at a given time sample. For the matrix above the answer would be 1.
>>
>> Is there a simple way to figure out if the species has never occurred
>> before and then sum them up?
>>
>> Thanks in advance,
>> Micheal
>>
>> --
>> Michael Denslow
>>
>> I.W. Carpenter Jr. Herbarium [BOON]
>> Department of Biology
>> Appalachian State University
>> Boone, North Carolina U.S.A.
>> -- AND --
>> Communications Manager
>> Southeast Regional Network of Expertise and Collections
>> sernec.org
>>
>> 36.214177, -81.681480 +/- 3103 meters
>>
>> ______________________________________________
>> 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.
>>
>
>
>
> --
> Jim Holtman
> Data Munger Guru
>
> What is the problem that you are trying to solve?
>



-- 
Michael Denslow

I.W. Carpenter Jr. Herbarium [BOON]
Department of Biology
Appalachian State University
Boone, North Carolina U.S.A.
-- AND --
Communications Manager
Southeast Regional Network of Expertise and Collections
sernec.org

36.214177, -81.681480 +/- 3103 meters