benrgillespie
2012-Sep-24 11:47 UTC
[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.
benrgillespie
2012-Sep-24 11:50 UTC
[R] Script to count unique values from two linked matricies
Note, trait richness would be 5 and not 4 at site 1.... perfectly demonstrating why I want to create a script rather than manually count! -- View this message in context: http://r.789695.n4.nabble.com/Script-to-count-unique-values-from-two-linked-matricies-tp4643979p4643980.html Sent from the R help mailing list archive at Nabble.com.
PIKAL Petr
2012-Sep-24 12:34 UTC
[R] Script to count unique values from two linked matricies
Hi I have no access to Nabble so it is difficult to understand what do you want.> -----Original Message----- > From: r-help-bounces at r-project.org [mailto:r-help-bounces at r- > project.org] On Behalf Of benrgillespie > Sent: Monday, September 24, 2012 1:47 PM > To: r-help at r-project.org > 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 aboutWhy not, everything is possible with R. Maybe you could provide data by dput(species). Maybe you want something like ?table or ?aggregate. Without data it is hard to say. Regards Petr> 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.
Benjamin Gillespie
2012-Sep-24 12:47 UTC
[R] Script to count unique values from two linked matricies
Hi Petr, Please see the attached .csv files - perhaps these will help, Thanks, 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: PIKAL Petr [petr.pikal at precheza.cz] Sent: 24 September 2012 13:34 To: Benjamin Gillespie; r-help at r-project.org Subject: RE: [R] Script to count unique values from two linked matricies Hi I have no access to Nabble so it is difficult to understand what do you want.> -----Original Message----- > From: r-help-bounces at r-project.org [mailto:r-help-bounces at r- > project.org] On Behalf Of benrgillespie > Sent: Monday, September 24, 2012 1:47 PM > To: r-help at r-project.org > 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 aboutWhy not, everything is possible with R. Maybe you could provide data by dput(species). Maybe you want something like ?table or ?aggregate. Without data it is hard to say. Regards Petr> 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.
benrgillespie
2012-Sep-24 13:14 UTC
[R] Script to count unique values from two linked matricies
Richness should look like this: <http://r.789695.n4.nabble.com/file/n4644004/trait_richness.jpg> -- View this message in context: http://r.789695.n4.nabble.com/Script-to-count-unique-values-from-two-linked-matricies-tp4643979p4644004.html Sent from the R help mailing list archive at Nabble.com.
Benjamin Gillespie
2012-Sep-25 08:11 UTC
[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.
Rui Barradas
2012-Sep-25 12:50 UTC
[R] 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) >> >> >> >> -- >> 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.