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 [smartpink...@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 gy...@leeds.ac.uk To: r-help@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@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@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.
Re: [R] 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(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 gy...@leeds.ac.ukwrote:
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 [smartpink...@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 gy...@leeds.ac.uk
To: r-help@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.
__
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Re: [R] Script to count unique values from two linked matricies
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-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Benjamin Gillespie Sent: Tuesday, September 25, 2012 10:11 AM To: arun; r-help@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 [smartpink...@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 gy...@leeds.ac.uk To: r-help@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@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@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@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.
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 [smartpink...@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 gy...@leeds.ac.uk To: r-help@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@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@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@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.
Re: [R] Script to count unique values from two linked matricies
Fantastic help - thanks guys.
Heramb, Pikal and Rui all came up with solutions.
I prefer Rui's as it seems the simplest.
I'm going to try and work through them to understand exactly what's going on at
each stage.
Thanks again all,
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: Heramb Gadgil [heramb.gad...@gmail.com]
Sent: 25 September 2012 10:38
To: Benjamin Gillespie
Cc: arun; r-help@r-project.org
Subject: Re: [R] 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.nahttp://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
gy...@leeds.ac.ukmailto:gy...@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 [smartpink...@yahoo.commailto:smartpink...@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 gy...@leeds.ac.ukmailto:gy...@leeds.ac.uk
To: r-help@r-project.orgmailto:r-help@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@r-project.orgmailto:R-help@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@r-project.orgmailto:R-help
Re: [R] Script to count unique values from two linked matricies
Excellent - thanks so much.
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 [smartpink...@yahoo.com]
Sent: 25 September 2012 14:22
To: Benjamin Gillespie
Cc: PIKAL Petr; Rui Barradas; Heramb Gadgil; R help
Subject: Re: [R] Script to count unique values from two linked matricies
Hi Ben,
Just a modification of Petr's solution with library(data.table):
dat1-data.frame(Species=paste0(Species,1:3),Site1=c(5,NA,4),Site2=c(3,2,4),Site3=c(NA,5,NA))
dat2-data.frame(Species=paste0(Species,1:3),Trait1=1:3,Trait2=c(2,4,2),Trait3=c(5,1,1))
library(data.table)
library(reshape)
datm-merge(melt(dat1),melt(dat2),by=Species)
temp-list(data.table(datm[datm[,2]==Site1
!is.na(datm[,3]),]),data.table(datm[datm[,2]==Site2
!is.na(datm[,3]),]),data.table(datm[datm[,2]==Site3 !is.na(datm[,3]),]))
Trait_Richness-unlist(lapply(temp, function(x)
sum(x[,list(length(unique(value.y))),list(variable.y)]$V1)))
dat3-data.frame(Site=colnames(dat1)[2:4],Trait_Richness=Trait_Richness)
dat3
# Site Trait_Richness
#1 Site1 5
#2 Site2 7
#3 Site3 3
A.K.
- Original Message -
From: Benjamin Gillespie gy...@leeds.ac.uk
To: Heramb Gadgil heramb.gad...@gmail.com
Cc: arun smartpink...@yahoo.com; r-help@r-project.org r-help@r-project.org
Sent: Tuesday, September 25, 2012 8:56 AM
Subject: RE: [R] Script to count unique values from two linked matricies
Fantastic help - thanks guys.
Heramb, Pikal and Rui all came up with solutions.
I prefer Rui's as it seems the simplest.
I'm going to try and work through them to understand exactly what's going on at
each stage.
Thanks again all,
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: Heramb Gadgil [heramb.gad...@gmail.com]
Sent: 25 September 2012 10:38
To: Benjamin Gillespie
Cc: arun; r-help@r-project.org
Subject: Re: [R] 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.nahttp://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
gy...@leeds.ac.ukmailto:gy...@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 [smartpink...@yahoo.commailto:smartpink...@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 gy
Re: [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 [ruipbarra...@sapo.pt] Sent: 25 September 2012 10:30 To: Benjamin Gillespie Cc: arun; r-help@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 [smartpink...@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 gy...@leeds.ac.uk To: r-help@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@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@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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
Re: [R] Script to count unique values from two linked matricies
Hi Ben,
Just a modification of Petr's solution with library(data.table):
dat1-data.frame(Species=paste0(Species,1:3),Site1=c(5,NA,4),Site2=c(3,2,4),Site3=c(NA,5,NA))
dat2-data.frame(Species=paste0(Species,1:3),Trait1=1:3,Trait2=c(2,4,2),Trait3=c(5,1,1))
library(data.table)
library(reshape)
datm-merge(melt(dat1),melt(dat2),by=Species)
temp-list(data.table(datm[datm[,2]==Site1
!is.na(datm[,3]),]),data.table(datm[datm[,2]==Site2
!is.na(datm[,3]),]),data.table(datm[datm[,2]==Site3 !is.na(datm[,3]),]))
Trait_Richness-unlist(lapply(temp, function(x)
sum(x[,list(length(unique(value.y))),list(variable.y)]$V1)))
dat3-data.frame(Site=colnames(dat1)[2:4],Trait_Richness=Trait_Richness)
dat3
# Site Trait_Richness
#1 Site1 5
#2 Site2 7
#3 Site3 3
A.K.
- Original Message -
From: Benjamin Gillespie gy...@leeds.ac.uk
To: Heramb Gadgil heramb.gad...@gmail.com
Cc: arun smartpink...@yahoo.com; r-help@r-project.org r-help@r-project.org
Sent: Tuesday, September 25, 2012 8:56 AM
Subject: RE: [R] Script to count unique values from two linked matricies
Fantastic help - thanks guys.
Heramb, Pikal and Rui all came up with solutions.
I prefer Rui's as it seems the simplest.
I'm going to try and work through them to understand exactly what's going on at
each stage.
Thanks again all,
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: Heramb Gadgil [heramb.gad...@gmail.com]
Sent: 25 September 2012 10:38
To: Benjamin Gillespie
Cc: arun; r-help@r-project.org
Subject: Re: [R] 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.nahttp://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
gy...@leeds.ac.ukmailto:gy...@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 [smartpink...@yahoo.commailto:smartpink...@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 gy...@leeds.ac.ukmailto:gy...@leeds.ac.uk
To: r-help@r-project.orgmailto:r-help@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
Re: [R] Script to count unique values from two linked matricies
You're good!
Thanks again :)
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 [smartpink...@yahoo.com]
Sent: 25 September 2012 17:04
To: Benjamin Gillespie
Cc: R help
Subject: Re: [R] Script to count unique values from two linked matricies
Hi Ben,
No problem.
The code could be collapsed to 2 steps:
library(data.table)
library(reshape)
datm-merge(melt(dat1),melt(dat2),by=Species)
dat3-data.frame(unlist(lapply(lapply(split(datm,datm$variable.x),function(x)
data.table(x[!is.na(x$value.x),])),function(x)
sum(x[,list(length(unique(value.y))),list(variable.y)]$V1
colnames(dat3)-Trait_Richness
dat3
# Trait_Richness
#Site1 5
#Site2 7
#Site3 3
A.K.
- Original Message -
From: Benjamin Gillespie gy...@leeds.ac.uk
To: arun smartpink...@yahoo.com
Cc: PIKAL Petr petr.pi...@precheza.cz; Rui Barradas ruipbarra...@sapo.pt;
Heramb Gadgil heramb.gad...@gmail.com; R help r-help@r-project.org
Sent: Tuesday, September 25, 2012 9:34 AM
Subject: RE: [R] Script to count unique values from two linked matricies
Excellent - thanks so much.
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 [smartpink...@yahoo.com]
Sent: 25 September 2012 14:22
To: Benjamin Gillespie
Cc: PIKAL Petr; Rui Barradas; Heramb Gadgil; R help
Subject: Re: [R] Script to count unique values from two linked matricies
Hi Ben,
Just a modification of Petr's solution with library(data.table):
dat1-data.frame(Species=paste0(Species,1:3),Site1=c(5,NA,4),Site2=c(3,2,4),Site3=c(NA,5,NA))
dat2-data.frame(Species=paste0(Species,1:3),Trait1=1:3,Trait2=c(2,4,2),Trait3=c(5,1,1))
library(data.table)
library(reshape)
datm-merge(melt(dat1),melt(dat2),by=Species)
temp-list(data.table(datm[datm[,2]==Site1
!is.na(datm[,3]),]),data.table(datm[datm[,2]==Site2
!is.na(datm[,3]),]),data.table(datm[datm[,2]==Site3 !is.na(datm[,3]),]))
Trait_Richness-unlist(lapply(temp, function(x)
sum(x[,list(length(unique(value.y))),list(variable.y)]$V1)))
dat3-data.frame(Site=colnames(dat1)[2:4],Trait_Richness=Trait_Richness)
dat3
# Site Trait_Richness
#1 Site1 5
#2 Site2 7
#3 Site3 3
A.K.
- Original Message -
From: Benjamin Gillespie gy...@leeds.ac.uk
To: Heramb Gadgil heramb.gad...@gmail.com
Cc: arun smartpink...@yahoo.com; r-help@r-project.org r-help@r-project.org
Sent: Tuesday, September 25, 2012 8:56 AM
Subject: RE: [R] Script to count unique values from two linked matricies
Fantastic help - thanks guys.
Heramb, Pikal and Rui all came up with solutions.
I prefer Rui's as it seems the simplest.
I'm going to try and work through them to understand exactly what's going on at
each stage.
Thanks again all,
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: Heramb Gadgil [heramb.gad...@gmail.com]
Sent: 25 September 2012 10:38
To: Benjamin Gillespie
Cc: arun; r-help@r-project.org
Subject: Re: [R] 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.nahttp://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
gy...@leeds.ac.ukmailto:gy...@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
Re: [R] Script to count unique values from two linked matricies
Hi Ben,
No problem.
The code could be collapsed to 2 steps:
library(data.table)
library(reshape)
datm-merge(melt(dat1),melt(dat2),by=Species)
dat3-data.frame(unlist(lapply(lapply(split(datm,datm$variable.x),function(x)
data.table(x[!is.na(x$value.x),])),function(x)
sum(x[,list(length(unique(value.y))),list(variable.y)]$V1
colnames(dat3)-Trait_Richness
dat3
# Trait_Richness
#Site1 5
#Site2 7
#Site3 3
A.K.
- Original Message -
From: Benjamin Gillespie gy...@leeds.ac.uk
To: arun smartpink...@yahoo.com
Cc: PIKAL Petr petr.pi...@precheza.cz; Rui Barradas ruipbarra...@sapo.pt;
Heramb Gadgil heramb.gad...@gmail.com; R help r-help@r-project.org
Sent: Tuesday, September 25, 2012 9:34 AM
Subject: RE: [R] Script to count unique values from two linked matricies
Excellent - thanks so much.
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 [smartpink...@yahoo.com]
Sent: 25 September 2012 14:22
To: Benjamin Gillespie
Cc: PIKAL Petr; Rui Barradas; Heramb Gadgil; R help
Subject: Re: [R] Script to count unique values from two linked matricies
Hi Ben,
Just a modification of Petr's solution with library(data.table):
dat1-data.frame(Species=paste0(Species,1:3),Site1=c(5,NA,4),Site2=c(3,2,4),Site3=c(NA,5,NA))
dat2-data.frame(Species=paste0(Species,1:3),Trait1=1:3,Trait2=c(2,4,2),Trait3=c(5,1,1))
library(data.table)
library(reshape)
datm-merge(melt(dat1),melt(dat2),by=Species)
temp-list(data.table(datm[datm[,2]==Site1
!is.na(datm[,3]),]),data.table(datm[datm[,2]==Site2
!is.na(datm[,3]),]),data.table(datm[datm[,2]==Site3 !is.na(datm[,3]),]))
Trait_Richness-unlist(lapply(temp, function(x)
sum(x[,list(length(unique(value.y))),list(variable.y)]$V1)))
dat3-data.frame(Site=colnames(dat1)[2:4],Trait_Richness=Trait_Richness)
dat3
# Site Trait_Richness
#1 Site1 5
#2 Site2 7
#3 Site3 3
A.K.
- Original Message -
From: Benjamin Gillespie gy...@leeds.ac.uk
To: Heramb Gadgil heramb.gad...@gmail.com
Cc: arun smartpink...@yahoo.com; r-help@r-project.org r-help@r-project.org
Sent: Tuesday, September 25, 2012 8:56 AM
Subject: RE: [R] Script to count unique values from two linked matricies
Fantastic help - thanks guys.
Heramb, Pikal and Rui all came up with solutions.
I prefer Rui's as it seems the simplest.
I'm going to try and work through them to understand exactly what's going on at
each stage.
Thanks again all,
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: Heramb Gadgil [heramb.gad...@gmail.com]
Sent: 25 September 2012 10:38
To: Benjamin Gillespie
Cc: arun; r-help@r-project.org
Subject: Re: [R] 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.nahttp://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
gy...@leeds.ac.ukmailto:gy...@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
Re: [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. __ R-help@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.
Re: [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.pi...@precheza.cz] Sent: 24 September 2012 13:34 To: Benjamin Gillespie; r-help@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-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of benrgillespie Sent: Monday, September 24, 2012 1:47 PM To: r-help@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 about Why 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@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@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] 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@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.
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-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of benrgillespie Sent: Monday, September 24, 2012 1:47 PM To: r-help@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 about Why 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@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@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.
Re: [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. __ R-help@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.
