Script to count unique values from two linked matricies

Hello,

You must run the line defining function countTrait first in order to 
create it. Then run the rest.

Rui Barradas
Em 25-09-2012 13:42, Benjamin Gillespie escreveu:
Hi Rui, thanks, but I get this:

result <- apply(presence, 2, function(x) apply(dat2[, -1]*x, 2, countTrait))
Error in match.fun(FUN) : object 'countTrait' not found

Any ideas what could be going wrong?

Thanks for your help,

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: Rui Barradas [ruipbarradas at sapo.pt]
Sent: 25 September 2012 10:30
To: Benjamin Gillespie
Cc: arun; r-help at r-project.org
Subject: Re: [R] Script to count unique values from two linked matricies

Hello,

Try the following.

countTrait <- function(x) length( unique(x[x != 0]) )

presence <- 1*(!is.na(dat1[-1]))
result <- apply(presence, 2, function(x) apply(dat2[, -1]*x, 2, countTrait))
result <- t(result)
rowSums(result)
#Site1 Site2 Site3
#   5     7     3

Hope this helps,

Rui Barradas
Em 25-09-2012 09:11, Benjamin Gillespie escreveu:
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]
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>
To: 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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