R help - Jan 2008 - Function for translation of a list into a matrix as used by ordination?

Hello.

Does anyone know of an existing function that takes a list in the form of:

Plot1 Species1    Abundance1
Plot1 Species2    Abundance2
Plot2 Species1    Abundance1
Plot2 Species3    Abundance3
.
.
.
PlotN SpeciesN    AbundanceN

and translates into a matrix in the form of

      Species1    Species2....      SpeciesN
Plot1 Abundance1  Abundance2...     AbundanceN
Plot2 Abundance1  Abundance2...     AbundanceN
.
.

.
PlotN AbundanceN  AbundanceN...     AbundanceN


This is a basic operation used in the initial stages of ordination etc of
ecological data (vegetation or other species) that is usually stored in a
database or flatfile in the list format above. It is similar to a cross
tabulation like the function xtabs(), however its useful to be able to
control whether a measured abundance for a taxa is included or a boolean
(presence/absence) for the taxa in a given plot.

Im new to such analyses in R, but before writing it myself hope or suspect
that such a function or library is out there (although I dont see it after
some quick searching in things like Vegan or BiodivesityR or labdsv).


Thanks
billy

Take a look at ?reshape - it is used to convert between 'long' and
'wide'
formats of data tables (frames). 

-Christos 
> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of 
> Billy_Schweiger at nps.gov
> Sent: Friday, January 25, 2008 4:30 PM
> To: r-help at r-project.org
> Subject: [R] Function for translation of a list into a matrix 
> as used byordination?
> 
> 
> Hello.
> 
> Does anyone know of an existing function that takes a list in 
> the form of:
> 
> Plot1 Species1    Abundance1
> Plot1 Species2    Abundance2
> Plot2 Species1    Abundance1
> Plot2 Species3    Abundance3
> .
> .
> .
> PlotN SpeciesN    AbundanceN
> 
> and translates into a matrix in the form of
> 
>       Species1    Species2....      SpeciesN
> Plot1 Abundance1  Abundance2...     AbundanceN
> Plot2 Abundance1  Abundance2...     AbundanceN
> .
> .
> 
> .
> PlotN AbundanceN  AbundanceN...     AbundanceN
> 
> 
> This is a basic operation used in the initial stages of 
> ordination etc of ecological data (vegetation or other 
> species) that is usually stored in a database or flatfile in 
> the list format above. It is similar to a cross tabulation 
> like the function xtabs(), however its useful to be able to 
> control whether a measured abundance for a taxa is included 
> or a boolean
> (presence/absence) for the taxa in a given plot.
> 
> Im new to such analyses in R, but before writing it myself 
> hope or suspect that such a function or library is out there 
> (although I dont see it after some quick searching in things 
> like Vegan or BiodivesityR or labdsv).
> 
> 
> Thanks
> billy
> 
> ______________________________________________
> 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.
> 
>

I think you can do this fairly easily with the reshape
package. Is this basically what you want?

x <- "Plot1 Species1    Abundance1
 Plot1 Species2    Abundance2
 Plot2 Species1    Abundance1
 Plot2 Species3    Abundance3 "
 
 xx <- read.table(textConnection(x), header=TRUE,
as.is=TRUE); xx
 names(xx) <- c("plot", "species", "abon")
  
 ab <- melt(xx, id=c("plot", "species"),
measured=c("abon"))
 
 cast(ab, plot~  species + variable)



--- Billy_Schweiger at nps.gov wrote:
> 
> Hello.
> 
> Does anyone know of an existing function that takes
> a list in the form of:
> 
> Plot1 Species1    Abundance1
> Plot1 Species2    Abundance2
> Plot2 Species1    Abundance1
> Plot2 Species3    Abundance3
> .
> .
> .
> PlotN SpeciesN    AbundanceN
> 
> and translates into a matrix in the form of
> 
>       Species1    Species2....      SpeciesN
> Plot1 Abundance1  Abundance2...     AbundanceN
> Plot2 Abundance1  Abundance2...     AbundanceN
> .
> .
> 
> .
> PlotN AbundanceN  AbundanceN...     AbundanceN
> 
> 
> This is a basic operation used in the initial stages
> of ordination etc of
> ecological data (vegetation or other species) that
> is usually stored in a
> database or flatfile in the list format above. It is
> similar to a cross
> tabulation like the function xtabs(), however its
> useful to be able to
> control whether a measured abundance for a taxa is
> included or a boolean
> (presence/absence) for the taxa in a given plot.
> 
> Im new to such analyses in R, but before writing it
> myself hope or suspect
> that such a function or library is out there
> (although I dont see it after
> some quick searching in things like Vegan or
> BiodivesityR or labdsv).
> 
> 
> Thanks
> billy
> 
> ______________________________________________
> 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 this also:

 noquote(tapply(x$Abundance, list(x$Plot, x$Species), paste))

On 25/01/2008, Billy_Schweiger at nps.gov <Billy_Schweiger at nps.gov>
wrote:
>
> Hello.
>
> Does anyone know of an existing function that takes a list in the form of:
>
> Plot1 Species1    Abundance1
> Plot1 Species2    Abundance2
> Plot2 Species1    Abundance1
> Plot2 Species3    Abundance3
> .
> .
> .
> PlotN SpeciesN    AbundanceN
>
> and translates into a matrix in the form of
>
>       Species1    Species2....      SpeciesN
> Plot1 Abundance1  Abundance2...     AbundanceN
> Plot2 Abundance1  Abundance2...     AbundanceN
> .
> .
>
> .
> PlotN AbundanceN  AbundanceN...     AbundanceN
>
>
> This is a basic operation used in the initial stages of ordination etc of
> ecological data (vegetation or other species) that is usually stored in a
> database or flatfile in the list format above. It is similar to a cross
> tabulation like the function xtabs(), however its useful to be able to
> control whether a measured abundance for a taxa is included or a boolean
> (presence/absence) for the taxa in a given plot.
>
> Im new to such analyses in R, but before writing it myself hope or suspect
> that such a function or library is out there (although I dont see it after
> some quick searching in things like Vegan or BiodivesityR or labdsv).
>
>
> Thanks
> billy
>
> ______________________________________________
> 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.
>

-- 
Henrique Dallazuanna
Curitiba-Paran?-Brasil
25? 25' 40" S 49? 16' 22" O

Thanks for all who commented on this question.

It turns out that there is a nice set of functions in library BiodiversityR
that translate a stack or list input data file to a community matrix:

import.from.Excel(file = file.choose(), sheet = "community", sitenames
"sites",
    column = "species", value = "abundance", factor =
"", level = "")
import.from.Access(file = file.choose(), table = "community",
sitenames "sites",
    column = "species", value = "abundance", factor =
"", level = "")

I believe the other contributions set to the list worked to varying degrees
as well.

billy