I've been trying to reshape this database but haven't succeed at it. I tried using loops but can't get it right. I just want to reshape my database from this matrix, to the one below, with only one column of data. Year Route Point Sp1 Sp2 Sp3 2004 123 123-1 0 1 0 2004 123 123-2 0 1 1 2004 123 123-10 1 1 0 What I want: Year Route Point 2004 123 123-1 Sp1 0 2004 123 123-2 Sp1 0 2004 123 123-10 Sp1 1 2004 123 123-1 Sp2 1 2004 123 123-2 Sp2 1 2004 123 123-10 Sp2 1 2004 123 123-1 Sp3 0 2004 123 123-2 Sp3 1 2004 123 123-10 Sp3 0 -- View this message in context: http://r.789695.n4.nabble.com/Presence-absence-data-from-matrix-to-single-column-tp4645271.html Sent from the R help mailing list archive at Nabble.com.
Presence/ absence data from matrix to single column
14 messages · arun, John Kane, Andrea Goijman +3 more
Hi,
Try this:
dat1<-read.table(text="
Year??? Route??? Point??? Sp1??? Sp2??? Sp3
2004??? 123??? 123-1??? 0??? 1??? 0
2004??? 123??? 123-2??? 0??? 1??? 1
2004??? 123??? 123-10??? 1??? 1??? 0
",header=TRUE,sep="",stringsAsFactors=FALSE)
library(reshape)
melt(dat1,id=c("Year","Route","Point"))
? Year Route? Point variable value
1 2004?? 123? 123-1????? Sp1???? 0
2 2004?? 123? 123-2????? Sp1???? 0
3 2004?? 123 123-10????? Sp1???? 1
4 2004?? 123? 123-1????? Sp2???? 1
5 2004?? 123? 123-2????? Sp2???? 1
6 2004?? 123 123-10????? Sp2???? 1
7 2004?? 123? 123-1????? Sp3???? 0
8 2004?? 123? 123-2????? Sp3???? 1
9 2004?? 123 123-10????? Sp3???? 0
A.K.
----- Original Message -----
From: agoijman <agoijman at cnia.inta.gov.ar>
To: r-help at r-project.org
Cc:
Sent: Saturday, October 6, 2012 11:03 AM
Subject: [R] Presence/ absence data from matrix to single column
I've been trying to reshape this database but haven't succeed at it. I tried
using loops but can't get it right. I just want to reshape my database from
this matrix, to the one below, with only one column of data.
Year??? Route??? Point??? Sp1??? Sp2??? Sp3
2004??? 123??? 123-1??? 0??? 1??? 0
2004??? 123??? 123-2??? 0??? 1??? 1
2004??? 123??? 123-10??? 1??? 1??? 0
What I want:
Year??? Route??? Point??? ??? ???
2004??? 123??? 123-1??? Sp1??? 0???
2004??? 123??? 123-2??? Sp1??? 0???
2004??? 123??? 123-10??? Sp1??? 1???
2004??? 123??? 123-1??? Sp2??? 1???
2004??? 123??? 123-2??? Sp2??? 1???
2004??? 123??? 123-10??? Sp2??? 1???
2004??? 123??? 123-1??? Sp3??? 0???
2004??? 123??? 123-2??? Sp3??? 1???
2004??? 123??? 123-10??? Sp3??? 0???
--
View this message in context: http://r.789695.n4.nabble.com/Presence-absence-data-from-matrix-to-single-column-tp4645271.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.
Try the reshape2 package. You will probablly have to install the package. install.packages("reshape2)
with your data as xx :
library(reshape2)
melt(xx, id =c("Year", "Route", "Point"))
seems to do what you want.
John Kane
Kingston ON Canada
-----Original Message----- From: agoijman at cnia.inta.gov.ar Sent: Sat, 6 Oct 2012 08:03:11 -0700 (PDT) To: r-help at r-project.org Subject: [R] Presence/ absence data from matrix to single column I've been trying to reshape this database but haven't succeed at it. I tried using loops but can't get it right. I just want to reshape my database from this matrix, to the one below, with only one column of data. Year Route Point Sp1 Sp2 Sp3 2004 123 123-1 0 1 0 2004 123 123-2 0 1 1 2004 123 123-10 1 1 0 What I want: Year Route Point 2004 123 123-1 Sp1 0 2004 123 123-2 Sp1 0 2004 123 123-10 Sp1 1 2004 123 123-1 Sp2 1 2004 123 123-2 Sp2 1 2004 123 123-10 Sp2 1 2004 123 123-1 Sp3 0 2004 123 123-2 Sp3 1 2004 123 123-10 Sp3 0 -- View this message in context: http://r.789695.n4.nabble.com/Presence-absence-data-from-matrix-to-single-column-tp4645271.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.
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Works fantastic!!! thank you SO much -- View this message in context: http://r.789695.n4.nabble.com/Presence-absence-data-from-matrix-to-single-column-tp4645271p4645302.html Sent from the R help mailing list archive at Nabble.com.
On 10/07/2012 01:03 AM, agoijman wrote:
I've been trying to reshape this database but haven't succeed at it. I tried using loops but can't get it right. I just want to reshape my database from this matrix, to the one below, with only one column of data. Year Route Point Sp1 Sp2 Sp3 2004 123 123-1 0 1 0 2004 123 123-2 0 1 1 2004 123 123-10 1 1 0 What I want: Year Route Point 2004 123 123-1 Sp1 0 2004 123 123-2 Sp1 0 2004 123 123-10 Sp1 1 2004 123 123-1 Sp2 1 2004 123 123-2 Sp2 1 2004 123 123-10 Sp2 1 2004 123 123-1 Sp3 0 2004 123 123-2 Sp3 1 2004 123 123-10 Sp3 0
Hi agoijman,
You can do this using the rep_n_stack function.
adat<-data.frame(Year=rep(2004,3),Route=rep(123,3),
Point=c("123-1","123-2","123-10"),Sp1=c(0,0,1),
Sp2=c(1,1,1),Sp3=c(0,1,0))
library(prettyR)
rep_n_stack(adat,c("Sp1","Sp2","Sp3"),
stack.names=c("Sp-names","Sp-values"))
Jim
Also reshape() will work:
adat<-data.frame(Year=rep(2004,3),Route=rep(123,3),
Point=c("123-1","123-2","123-10"),Sp1=c(0,0,1),
Sp2=c(1,1,1),Sp3=c(0,1,0))
reshape(adat, varying=4:6, v.name="Sp-value",
times=c("Sp1", "Sp2", "Sp3"), idvar="Point",
timevar="Sp-name", direction="long")
----------------------------------------------
David L Carlson
Associate Professor of Anthropology
Texas A&M University
College Station, TX 77843-4352
-----Original Message----- From: r-help-bounces at r-project.org [mailto:r-help-bounces at r- project.org] On Behalf Of Jim Lemon Sent: Saturday, October 06, 2012 7:36 PM To: agoijman Cc: r-help at r-project.org Subject: Re: [R] Presence/ absence data from matrix to single column On 10/07/2012 01:03 AM, agoijman wrote:
I've been trying to reshape this database but haven't succeed at it.
I tried
using loops but can't get it right. I just want to reshape my
database from
this matrix, to the one below, with only one column of data. Year Route Point Sp1 Sp2 Sp3 2004 123 123-1 0 1 0 2004 123 123-2 0 1 1 2004 123 123-10 1 1 0 What I want: Year Route Point 2004 123 123-1 Sp1 0 2004 123 123-2 Sp1 0 2004 123 123-10 Sp1 1 2004 123 123-1 Sp2 1 2004 123 123-2 Sp2 1 2004 123 123-10 Sp2 1 2004 123 123-1 Sp3 0 2004 123 123-2 Sp3 1 2004 123 123-10 Sp3 0
Hi agoijman,
You can do this using the rep_n_stack function.
adat<-data.frame(Year=rep(2004,3),Route=rep(123,3),
Point=c("123-1","123-2","123-10"),Sp1=c(0,0,1),
Sp2=c(1,1,1),Sp3=c(0,1,0))
library(prettyR)
rep_n_stack(adat,c("Sp1","Sp2","Sp3"),
stack.names=c("Sp-names","Sp-values"))
Jim
______________________________________________ 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.
The problem with that, is that I just wrote an example of my database, but I have around 250 species and more than 500 sites. In the approach you show me, it looks like I have to enter every species name and sites individually, right? -- View this message in context: http://r.789695.n4.nabble.com/Presence-absence-data-from-matrix-to-single-column-tp4645271p4645331.html Sent from the R help mailing list archive at Nabble.com.
Hello,
I haven't been following this thread but apparently the answer to your
worries is no.
You can use a combination of names() and grep() to sort it out.
something like
#nms <- names(adat)
nms <- c("Year", "Route", "Point", paste0("Sp", 1:250))
pattern <- "^Sp[[:digit:]]+$"
whichCols <- grep(pattern, nms)
whichNames <- nms[whichCols]
reshape(..., varying = whichCols, times = whichNames, ...)
Hope this helps,
Rui Barradas
Em 07-10-2012 15:35, agoijman escreveu:
The problem with that, is that I just wrote an example of my database, but I have around 250 species and more than 500 sites. In the approach you show me, it looks like I have to enter every species name and sites individually, right? -- View this message in context: http://r.789695.n4.nabble.com/Presence-absence-data-from-matrix-to-single-column-tp4645271p4645331.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.
Hi,
I guess you are not talking about the melt() method.
dat1<-read.table(text="
Year??? Route??? Point??? Sp1??? Sp2??? Sp3
2004??? 123??? 123-1??? 0??? 1??? 0
2004??? 123??? 123-2??? 0??? 1??? 1
2004??? 123??? 123-10??? 1??? 1??? 0
",header=TRUE,sep="",stringsAsFactors=FALSE)
#If all the Sp columns are located next to another as shown in your example dataset, then you can also try this:
name1<-unlist(strsplit(paste(colnames(dat1)[4:6],collapse=" ")," "))
reshape(dat1,varying=4:6,v.name="Sp-value",times=name1,timevar="Sp-name",idvar=c("Year","Route","Point"),direction="long")
A.K.
----- Original Message -----
From: Rui Barradas <ruipbarradas at sapo.pt>
To: agoijman <agoijman at cnia.inta.gov.ar>
Cc: r-help at r-project.org
Sent: Sunday, October 7, 2012 2:32 PM
Subject: Re: [R] Presence/ absence data from matrix to single column
Hello,
I haven't been following this thread but apparently the answer to your
worries is no.
You can use a combination of names() and grep() to sort it out.
something like
#nms <- names(adat)
nms <- c("Year", "Route", "Point", paste0("Sp", 1:250))
pattern <- "^Sp[[:digit:]]+$"
whichCols <- grep(pattern, nms)
whichNames <- nms[whichCols]
reshape(..., varying = whichCols, times = whichNames, ...)
Hope this helps,
Rui Barradas
Em 07-10-2012 15:35, agoijman escreveu:
The problem with that, is that I just wrote an example of my database, but I have around 250 species and more than 500 sites. In the approach you show me, it looks like I have to enter every species name and sites individually, right? -- View this message in context: http://r.789695.n4.nabble.com/Presence-absence-data-from-matrix-to-single-column-tp4645271p4645331.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.
You should keep the context of your thread intact for those of us using email instead of Nabble. The locations were not listed individually anywhere in the reshape() command. I listed Point as the id variable so reshape would use that to create row names, but if you delete idvar="Point", reshape will give each row a consecutive number followed by the species name or number. I did list the species names individually in the times= argument to make things a bit clearer since reshape() can be a confusing command at first. But this would work as well: reshape(adat, varying=4:6, v.name="Sp-value", times=names(adat)[4:6], idvar="Point", timevar="Sp-name", direction="long") ---------------------------------------------- David L Carlson Associate Professor of Anthropology Texas A&M University College Station, TX 77843-4352
Date: Sun, 7 Oct 2012 07:35:42 -0700 (PDT) From: agoijman <agoijman at cnia.inta.gov.ar> To: r-help at r-project.org Subject: Re: [R] Presence/ absence data from matrix to single column The problem with that, is that I just wrote an example of my database, but
I
have around 250 species and more than 500 sites. In the approach you show me, it looks like I have to enter every species name and sites
individually,
right? -- View this message in context:
http://r.789695.n4.nabble.com/Presence-absence-data-from-matrix-to-single-co lumn-tp4645271p4645331.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.
-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
project.org] On Behalf Of David L Carlson
Sent: Saturday, October 06, 2012 10:25 PM
To: 'Jim Lemon'; 'agoijman'
Cc: r-help at r-project.org
Subject: Re: [R] Presence/ absence data from matrix to single column
Also reshape() will work:
adat<-data.frame(Year=rep(2004,3),Route=rep(123,3),
Point=c("123-1","123-2","123-10"),Sp1=c(0,0,1),
Sp2=c(1,1,1),Sp3=c(0,1,0))
reshape(adat, varying=4:6, v.name="Sp-value",
times=c("Sp1", "Sp2", "Sp3"), idvar="Point",
timevar="Sp-name", direction="long")
----------------------------------------------
David L Carlson
Associate Professor of Anthropology
Texas A&M University
College Station, TX 77843-4352
-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
project.org] On Behalf Of Jim Lemon
Sent: Saturday, October 06, 2012 7:36 PM
To: agoijman
Cc: r-help at r-project.org
Subject: Re: [R] Presence/ absence data from matrix to single column
On 10/07/2012 01:03 AM, agoijman wrote:
I've been trying to reshape this database but haven't succeed at
it.
I tried
using loops but can't get it right. I just want to reshape my
database from
this matrix, to the one below, with only one column of data.
Year Route Point Sp1 Sp2 Sp3
2004 123 123-1 0 1 0
2004 123 123-2 0 1 1
2004 123 123-10 1 1 0
What I want:
Year Route Point
2004 123 123-1 Sp1 0
2004 123 123-2 Sp1 0
2004 123 123-10 Sp1 1
2004 123 123-1 Sp2 1
2004 123 123-2 Sp2 1
2004 123 123-10 Sp2 1
2004 123 123-1 Sp3 0
2004 123 123-2 Sp3 1
2004 123 123-10 Sp3 0
Hi agoijman,
You can do this using the rep_n_stack function.
adat<-data.frame(Year=rep(2004,3),Route=rep(123,3),
Point=c("123-1","123-2","123-10"),Sp1=c(0,0,1),
Sp2=c(1,1,1),Sp3=c(0,1,0))
library(prettyR)
rep_n_stack(adat,c("Sp1","Sp2","Sp3"),
stack.names=c("Sp-names","Sp-values"))
Jim
______________________________________________
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.
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Hello, If all your species have different names, you can allways try one of 1. if the non-species follow a pattern, negate those columns and you'll have the species columns. 2. are the species the last columns? Use positional referencing. Rui Barradas Em 08-10-2012 00:16, Andrea Goijman escreveu:
Ill try this one as well.
And I guess the one below is not going to work, because all my species
have different names.
Thanks!
#nms <- names(adat)
nms <- c("Year", "Route", "Point", paste0("Sp", 1:250))
pattern <- "^Sp[[:digit:]]+$"
whichCols <- grep(pattern, nms)
whichNames <- nms[whichCols]
reshape(..., varying = whichCols, times = whichNames, ...)
On Sun, Oct 7, 2012 at 3:02 PM, arun <smartpink111 at yahoo.com> wrote:
Hi,
I guess you are not talking about the melt() method.
dat1<-read.table(text="
Year Route Point Sp1 Sp2 Sp3
2004 123 123-1 0 1 0
2004 123 123-2 0 1 1
2004 123 123-10 1 1 0
",header=TRUE,sep="",stringsAsFactors=FALSE)
#If all the Sp columns are located next to another as shown in your
example dataset, then you can also try this:
name1<-unlist(strsplit(paste(colnames(dat1)[4:6],collapse=" ")," "))
reshape(dat1,varying=4:6,v.name
="Sp-value",times=name1,timevar="Sp-name",idvar=c("Year","Route","Point"),direction="long")
A.K.
----- Original Message -----
From: Rui Barradas <ruipbarradas at sapo.pt>
To: agoijman <agoijman at cnia.inta.gov.ar>
Cc: r-help at r-project.org
Sent: Sunday, October 7, 2012 2:32 PM
Subject: Re: [R] Presence/ absence data from matrix to single column
Hello,
I haven't been following this thread but apparently the answer to your
worries is no.
You can use a combination of names() and grep() to sort it out.
something like
#nms <- names(adat)
nms <- c("Year", "Route", "Point", paste0("Sp", 1:250))
pattern <- "^Sp[[:digit:]]+$"
whichCols <- grep(pattern, nms)
whichNames <- nms[whichCols]
reshape(..., varying = whichCols, times = whichNames, ...)
Hope this helps,
Rui Barradas
Em 07-10-2012 15:35, agoijman escreveu:
The problem with that, is that I just wrote an example of my database,
but I
have around 250 species and more than 500 sites. In the approach you show me, it looks like I have to enter every species name and sites
individually,
right? -- View this message in context:
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.
HI,
Sorry, I complicated a code where it was not required at all.
Just using colnames(dat1)[4:6] or names(dat1)[4:6] should work if the species columns are adjacent to each other.
reshape(dat1,varying=4:6,v.name="Sp-value",times=colnames(dat1)[4:6],timevar="Sp-name",idvar=c("Year","Route","Point"),direction="long")
#or
reshape(dat1,varying=4:6,v.name="Sp-value",times=names(dat1)[4:6],timevar="Sp-name",idvar=c("Year","Route","Point"),direction="long")
A.K.
From: Andrea Goijman <agoijman at cnia.inta.gov.ar>
To: arun <smartpink111 at yahoo.com>
Cc: Rui Barradas <ruipbarradas at sapo.pt>; R help <r-help at r-project.org>
Sent: Sunday, October 7, 2012 7:16 PM
Subject: Re: [R] Presence/ absence data from matrix to single column
To: arun <smartpink111 at yahoo.com>
Cc: Rui Barradas <ruipbarradas at sapo.pt>; R help <r-help at r-project.org>
Sent: Sunday, October 7, 2012 7:16 PM
Subject: Re: [R] Presence/ absence data from matrix to single column
Ill try this one as well.
And I guess the one below is not going ?to work, because all my species have different names.
Thanks!
#nms <- names(adat)
nms <- c("Year", "Route", "Point", paste0("Sp", 1:250))
pattern <- "^Sp[[:digit:]]+$"
whichCols <- grep(pattern, nms)
whichNames <- nms[whichCols]
reshape(..., varying = whichCols, times = whichNames, ...)
On Sun, Oct 7, 2012 at 3:02 PM, arun <smartpink111 at yahoo.com> wrote:
Hi,
>I guess you are not talking about the melt() method.
>dat1<-read.table(text="
>
>Year??? Route??? Point??? Sp1??? Sp2??? Sp3
>2004??? 123??? 123-1??? 0??? 1??? 0
>2004??? 123??? 123-2??? 0??? 1??? 1
>2004??? 123??? 123-10??? 1??? 1??? 0
>",header=TRUE,sep="",stringsAsFactors=FALSE)
>
>
>#If all the Sp columns are located next to another as shown in your example dataset, then you can also try this:
>name1<-unlist(strsplit(paste(colnames(dat1)[4:6],collapse=" ")," "))
>reshape(dat1,varying=4:6,v.name="Sp-value",times=name1,timevar="Sp-name",idvar=c("Year","Route","Point"),direction="long")
>
>
>A.K.
>
>
>
>
>
>
>----- Original Message -----
>
>From: Rui Barradas <ruipbarradas at sapo.pt>
>To: agoijman <agoijman at cnia.inta.gov.ar>
>Cc: r-help at r-project.org
>Sent: Sunday, October 7, 2012 2:32 PM
>Subject: Re: [R] Presence/ absence data from matrix to single column
>
>Hello,
>
>I haven't been following this thread but apparently the answer to your
>worries is no.
>You can use a combination of names() and grep() to sort it out.
>something like
>
>#nms <- names(adat)
>nms <- c("Year", "Route", "Point", paste0("Sp", 1:250))
>
>pattern <- "^Sp[[:digit:]]+$"
>whichCols <- grep(pattern, nms)
>whichNames <- nms[whichCols]
>
>reshape(..., varying = whichCols, times = whichNames, ...)
>
>
>Hope this helps,
>
>Rui Barradas
>Em 07-10-2012 15:35, agoijman escreveu:
>> The problem with that, is that I just wrote an example of my database, but I
>> have around 250 species and more than 500 sites. In the approach you show
>> me, it looks like I have to enter every species name and sites individually,
>> right?
>>
>>
>>
>> --
>> View this message in context: http://r.789695.n4.nabble.com/Presence-absence-data-from-matrix-to-single-column-tp4645271p4645331.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.
>
>
---Lic. Andrea Paula Goijman Grupo Ecolog?a y Gesti?n Ambiental de la Biodiversidad IRB - INTA Castelar, Argentina agoijman at cnia.inta.gov.arhttp://inta.gob.ar/personas/goijman.andrea/ PhD Candidate Georgia Cooperative Fish and Wildlife Research Unit D.B. Warnell School of Forestry and Natural Resources University of Georgia Athens, GA 30602 USA Tel. +706.206.4805 andreapg at uga.edu
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