Elaine Kuo
2013-Sep-20 23:14 UTC
[R] search species with all absence in a presence-absence matrix
Dear list I have a matrix composed of islandID as rows and speciesID as columns. IslandID: Island A, B, C….O (15 islands in total) SpeciesID: D0001, D0002, D0003….D0100 (100 species in total) The cell of the matrix describes presence (1) or absence (0) of the species in an island. Now I would like to search the species with absence (0) in all the islands (Island A to Island O.) Please kindly advise the R code for the search purpose. Thank you. Elaine [[alternative HTML version deleted]]
John Kane
2013-Sep-20 23:40 UTC
[R] search species with all absence in a presence-absence matrix
Once you learn to use dput() I am sure someone will be happy to help you. http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example John Kane Kingston ON Canada> -----Original Message----- > From: elaine.kuo.tw at gmail.com > Sent: Sat, 21 Sep 2013 07:14:38 +0800 > To: r-help at r-project.org > Subject: [R] search species with all absence in a presence-absence matrix > > Dear list > > > > I have a matrix composed of islandID as rows and speciesID as columns. > > IslandID: Island A, B, C?.O (15 islands in total) > > SpeciesID: D0001, D0002, D0003?.D0100 (100 species in total) > > > > The cell of the matrix describes presence (1) or absence (0) of the > species > in an island. > > > > Now I would like to search the species with absence (0) > > in all the islands (Island A to Island O.) > > > > Please kindly advise the R code for the search purpose. > > Thank you. > > > > Elaine > > [[alternative HTML version deleted]] > > ______________________________________________ > 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.____________________________________________________________ FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
arun
2013-Sep-21 00:57 UTC
[R] search species with all absence in a presence-absence matrix
Hi,
Try this:
?set.seed(248)
?lst1<- lapply(1:1000,function(i) matrix(
sample(0:1,15*100,replace=TRUE),ncol=100,dimnames=list(paste("Island",LETTERS[1:15]),?
paste0("D",sprintf("%04d",1:100)))))
?lst2<-lst1[sapply(lst1,function(x) any(colSums(x)==0))]
##The above steps are just to create some matrices with zeros in all the
"islands"
mat1<-lst2[[1]]
?mat1[,colSums(mat1)==0,drop=FALSE]
#???????? D0038
#Island A???? 0
#Island B???? 0
#Island C???? 0
#Island D???? 0
#Island E???? 0
#Island F???? 0
#Island G???? 0
#Island H???? 0
#Island I???? 0
#Island J???? 0
#Island K???? 0
#Island L???? 0
#Island M???? 0
#Island N???? 0
#Island O???? 0
colnames(mat1)[colSums(mat1)==0]
#[1] "D0038"
?mat2<-lst2[[3]]
?colnames(mat2)[colSums(mat2)==0]
#[1] "D0086"
A.K.
----- Original Message -----
From: Elaine Kuo <elaine.kuo.tw at gmail.com>
To: "r-help at r-project.org" <r-help at r-project.org>
Cc:
Sent: Friday, September 20, 2013 7:14 PM
Subject: [R] search species with all absence in a presence-absence matrix
Dear list
I have a matrix composed of islandID as rows and speciesID as columns.
IslandID: Island A, B, C?.O (15 islands in total)
SpeciesID: D0001, D0002, D0003?.D0100 (100 species in total)
The cell of the matrix describes presence (1) or absence (0) of the species
in an island.
Now I would like to search the species with absence (0)
in all the islands (Island A to Island O.)
Please kindly advise the R code for the search purpose.
Thank you.
Elaine
??? [[alternative HTML version deleted]]
______________________________________________
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.
arun
2013-Sep-21 15:51 UTC
[R] search species with all absence in a presence-absence matrix
Hi Elaine,
#You can either convert the .xls dataset to .csv and read it with ?read.csv() or
use one of the packages to read excel dataset
library(XLConnect)
wb<- loadWorkbook("is_matrix.xls")
dataRM<- readWorksheet(wb,sheet="is_matrix",rownames=1)
dim(dataRM)
#[1] 22 23
?mat1<- as.matrix(dataRM)
matSub<- mat1[,colSums(mat1)==0,drop=FALSE]
?head(matSub,3)
#???????? D0008 D0009 D0010 D0011 D0012 D3396
#Sakhalin???? 0???? 0???? 0???? 0???? 0???? 0
#Hokkaido???? 0???? 0???? 0???? 0???? 0???? 0
#Korea??????? 0???? 0???? 0???? 0???? 0???? 0
colnames(mat1)[colSums(mat1)==0]
#[1] "D0008" "D0009" "D0010" "D0011"
"D0012" "D3396"
#I used lst1, lst2 etc just to create some data.
A.K.
________________________________
From: Elaine Kuo <elaine.kuo.tw at gmail.com>
To: arun <smartpink111 at yahoo.com>
Sent: Saturday, September 21, 2013 7:10 AM
Subject: Re: [R] search species with all absence in a presence-absence matrix
Hello Arun,
Thanks for the code.
I replaced my file (dataRM) with lst2 but
an error showed up.
It said
Error in colSums(mat1): x must be at an
array or at least two dimensions
I am sure the x (dataRM) is two-dimension.
Please kindly advise any code modification.
Also, I attach part of my data in the
e-mail.
Thank you again.
Elaine
Code
load("f:/b_W_line/R_workspace/R_workspace_R_4874/R_workspace_RM/dataset_RM_3546.RData")
?dim(dataRM)
?str(dataRM)
?mat1<-dataRM[[1]]
?mat1[,colSums(mat1)==0,drop=FALSE](error)
?colnames(mat1)[colSums(mat1)==0]
On Sat, Sep 21, 2013 at 8:57 AM, arun <smartpink111 at yahoo.com> wrote:
Hi,>Try this:
>
>?set.seed(248)
>?lst1<- lapply(1:1000,function(i) matrix(
sample(0:1,15*100,replace=TRUE),ncol=100,dimnames=list(paste("Island",LETTERS[1:15]),?
paste0("D",sprintf("%04d",1:100)))))
>?lst2<-lst1[sapply(lst1,function(x) any(colSums(x)==0))]
>##The above steps are just to create some matrices with zeros in all the
"islands"
>mat1<-lst2[[1]]
>?mat1[,colSums(mat1)==0,drop=FALSE]
>#???????? D0038
>#Island A???? 0
>#Island B???? 0
>#Island C???? 0
>#Island D???? 0
>#Island E???? 0
>#Island F???? 0
>#Island G???? 0
>#Island H???? 0
>#Island I???? 0
>#Island J???? 0
>#Island K???? 0
>#Island L???? 0
>#Island M???? 0
>#Island N???? 0
>#Island O???? 0
>colnames(mat1)[colSums(mat1)==0]
>#[1] "D0038"
>?mat2<-lst2[[3]]
>?colnames(mat2)[colSums(mat2)==0]
>#[1] "D0086"
>
>A.K.
>
>
>
>
>
>----- Original Message -----
>From: Elaine Kuo <elaine.kuo.tw at gmail.com>
>To: "r-help at r-project.org" <r-help at r-project.org>
>Cc:
>Sent: Friday, September 20, 2013 7:14 PM
>Subject: [R] search species with all absence in a presence-absence matrix
>
>
>Dear list
>
>
>
>I have a matrix composed of islandID as rows and speciesID as columns.
>
>IslandID: Island A, B, C?.O (15 islands in total)
>
>SpeciesID: D0001, D0002, D0003?.D0100 (100 species in total)
>
>
>
>The cell of the matrix describes presence (1) or absence (0) of the species
>in an island.
>
>
>
>Now I would like to search the species with absence (0)
>
>in all the islands (Island A to Island O.)
>
>
>
>Please kindly advise the R code for the search purpose.
>
>Thank you.
>
>
>
>Elaine
>
>
>??? [[alternative HTML version deleted]]
>
>______________________________________________
>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.
>
>?????