[R] Script to count unique values from two linked matricies

[PIKAL Petr]

Hi

thanks for data. Probably others can come with better solution

with 

library(reshape)

you can put your data to better form

dat2.m<-melt(dat2)
dat1.m<-melt(dat1)

merge them
dat<-merge(dat1.m, dat2.m, by="Species")


and finally compute required values

select one site
temp<-dat[dat[,2]=="Site3"& !is.na(dat[,3]),]

and compute unique values
length(unlist(aggregate(temp$value.y, list(temp$variable.y), unique)$x))

It is not canned solution as I do not have much time to think it over, but if you do not have too much sites you could compute it in simple for cycle.

Regards
Petr


> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Benjamin Gillespie
> Sent: Tuesday, September 25, 2012 10:11 AM
> To: arun; r-help at r-project.org
> Subject: Re: [R] Script to count unique values from two linked
> matricies
> 
> 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)
> 
> 
> 
> --
> View this message in context: http://r.789695.n4.nabble.com/Script-to-
> count-unique-values-from-two-linked-matricies-tp4643979.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> ______________________________________________
> 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.