Species CoOccurance

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Lanna,

I don't know exactly what do you mean by co-occurrence data frame, but
if you'd like to get a species-by-species matrix, in which you count
the co-occurrences of the species (columns in the sites-by-species
community matrix) with each other, you can use the crossprod function
or the %*% operator for a presence/absence matrix:

m <- matrix(rbinom(15,1,0.6),5,3)
t(m) %*% m
crossprod(m, m)

HTH,

Peter
Hello All,

I've been sifting through tons of R Documentation, trying to find a command
that converts a community matrix dataset into a species pair co-occurance
data frame, and have failed miserably to find one. ?Does a function already
exist in one of the community analysis packages?

Thanks in advance for your response!

--
Lanna Jin

lannajin at gmail.com
510-898-8525

? ? ? ?[[alternative HTML version deleted]]

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Lanna Jin <lannajin at gmail.com> writes:
Hi Peter,

Thanks for your quick response.  I am working with a dataframe that has
columns of Year, Location, Type (pertains to type of location), Species, and
Presence/Absence.  What I'm interested in doing is generating a data frame
that would not lose the "Year" , "Location" and "Type" data.  I would
ultimately like it to have the columns: "Year", "Location", "Type",
"SpeciesA", "SpeciesB", and "Co-occurance", where Co-occurance is either a 0
or 1 for if the species co-occur at the particular location at that exact
particular point in time.

Is there a function that exists out there that could quickly convert my data
into this form?  Or do I have to generate my own?
mydata$cooccur <- mydata$SpeciesA & mydata$SpeciesB

Where 'mydata' is the name of your dataframe.

Tyler