Script to count unique values from two linked matricies

We can have something like this;

Data1<-data.frame(Site1=c(5,NA,4),Site2=c(3,2,4),Site3=c(NA,5,NA))
Data2<-data.frame(TraitType1=c(1,2,3),TraitType2=c(2,4,2),TraitType3=c(5,1,1))

rownames(Data1)<-paste("Species",1:3)

rownames(Data2)<-paste("Species",1:3)

User_Defined=function(dat1,dat2){c1=ncol(dat1)

out=NULL

dummy=lapply(1:c1,function(x){step1=dat1[,x]

step2=dat2[which(is.na<http://is.na>(step1)==F),]

step3=length(unlist(apply(step2,2,unique)))

out<<-c(out,step3)

})

Final<-data.frame(TraitRichness=out)

rownames(Final)<-paste('Site',1:3)

Final_Table<<-Final

}

User_Defined(Data1,Data2)

Final_Table


I hope this is what you need.

Best,
Heramb

On Tue, Sep 25, 2012 at 1:41 PM, Benjamin Gillespie <gybrg at leeds.ac.uk<mailto:gybrg at leeds.ac.uk>> wrote:
Hi,

Thanks for helping me with this one.

To save you time, the following is the code for the tables I uploaded as jpegs that you may not have received:

dat1<-data.frame(Species=paste("Species",1:3),Site1=c(5,NA,4),Site2=c(3,2,4),Site3=c(NA,5,NA))
dat2<-data.frame(Species=paste("Species",1:3),TraitType1=c(1,2,3),TraitType2=c(2,4,2),TraitType3=c(5,1,1))
dat3<-data.frame(Site=paste("Site",1:3),Trait_Richness=c(5,7,3))

So,

I have two matricies, dat1 and dat2.

Dat1 is a species abundance matrix. Dat2 is a species trait matrix.

I want to create dat3 through use of a script.

Dat 3 is a count of unique traits observed at each site. i.e. at site 1, species 1 and 3 are present (ass seen in dat1). Species 1 has traits: 1, 2 and 5 for trait types 1, 2 and 3 respectively. Species 3 has traits: 3, 2 and 1 for trait types 1, 2 and 3 respectively.

So, at site 1:

For trait type 1, 2 unique traits were observed. For trait type 2, 1 unique trait was observed (both species 1 and 3 were classed as "1") and for trait type 3, 2 unique traits (trait richness) were observed; thus, 2+1+2=5.

and so on... so at site 2, all three species were observed...

For trait type 1, 3 unique traits were observed (1, 2, 3), for trait type 2, 2 unique traits were observed (2, 4, 2) and for trait type 3, 2 unique traits were observed (5, 1, 1). So, for site 2, trait richness is 7 (3+2+2) traits.

I hope this helps to explain, please let me know if you need any further information,

Ben Gillespie
Research Postgraduate

School of Geography
University of Leeds
Leeds
LS2 9JT

Tel: +44(0)113 34 33345
Mob: +44(0)770 868 7641
http://www.geog.leeds.ac.uk/
________________________________________
From: arun [smartpink111 at yahoo.com<mailto:smartpink111 at yahoo.com>]
Sent: 24 September 2012 19:36
To: Benjamin Gillespie
Subject: Re: [R] Script to count unique values from two linked matricies

HI Ben,

Sorry,I couldn't understand how you counted the trait richness.  Could you elaborate?
A.K.


----- Original Message -----
From: benrgillespie <gybrg at leeds.ac.uk<mailto:gybrg at leeds.ac.uk>>
To: r-help at r-project.org<mailto:r-help at r-project.org>
Cc:
Sent: Monday, September 24, 2012 7:47 AM
Subject: [R] Script to count unique values from two linked matricies

I hope you can help with this one.

I have two matricies:

1. A species abundance matrix:

<http://r.789695.n4.nabble.com/file/n4643979/2species_matrix.jpg>

2. A species trait score matrix:

<http://r.789695.n4.nabble.com/file/n4643979/2trait_matrix.jpg>

The trait matrix lists trait scores for each species as listed in the
species abundance matrix.

I would like to create a script that would effectively count the unique
traits (trait richness) for each site and produce an output like this:

<http://r.789695.n4.nabble.com/file/n4643979/trait_richness.jpg>

Firstly, is this possible in R? Secondly, if so, how would you go about
writing a script to achieve my aim?

Many thanks in advance, please let me know if you need further information.

Ben Gillespie (Research Postgraduate)



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and provide commented, minimal, self-contained, reproducible code.