[R] merge matrix row data

arun smartpink111 at yahoo.com
Thu Aug 1 01:15:45 CEST 2013


Hi Elaine, 

In that case:
Do you have "GID" in the "IslandA" and "IslandB"s?

IslandA<-c("GID 1", "GID 5")
IslandB<- c("GID 2", "GID 4", "GID 7")

If there is no change in the two "Islands", then using the same dataset:

mat1<- as.matrix(read.table(text="
D0989  D9820  D5629  D4327  D2134
GID_1    1        0        0      1      0
GID_2    0        1        1      0      0
GID_4    0        0        1      0      0
GID_5    1        1        0      0      0
GID_7    0        1        0      0      1
",sep="",header=TRUE))

row.names(mat1)<- gsub(".*\\_","",row.names(mat1)) #to replace the "GID_" from the row.names()
 mat1
#  D0989 D9820 D5629 D4327 D2134
#1     1     0     0     1     0
#2     0     1     1     0     0
#4     0     0     1     0     0
#5     1     1     0     0     0
#7     0     1     0     0     1
 IslandA<-c("GID 1", "GID 5")
 IslandB<- c("GID 2", "GID 4", "GID 7")
res<-t(sapply(c("IslandA","IslandB"),function(x) {x1<- mat1[match(gsub(".*\\s+","",get(x)),row.names(mat1)),];(!!colSums(x1))*1}))
res
 #       D0989 D9820 D5629 D4327 D2134
#IslandA     1     1     0     1     0
#IslandB     0     1     1     0     1


Regarding the use of "!!colSums()"
You can check these:

 t(sapply(c("IslandA","IslandB"),function(x) {x1<- mat1[match(gsub(".*\\s+","",get(x)),row.names(mat1)),];!colSums(x1)}))
#        D0989 D9820 D5629 D4327 D2134
#IslandA FALSE FALSE  TRUE FALSE  TRUE
#IslandB  TRUE FALSE FALSE  TRUE FALSE
 
t(sapply(c("IslandA","IslandB"),function(x) {x1<- mat1[match(gsub(".*\\s+","",get(x)),row.names(mat1)),];!!colSums(x1)}))
#        D0989 D9820 D5629 D4327 D2134
#IslandA  TRUE  TRUE FALSE  TRUE FALSE
#IslandB FALSE  TRUE  TRUE FALSE  TRUE

# "*1" will replace TRUE with 1 and FALSE with 0.

A.K.






________________________________
From: Elaine Kuo <elaine.kuo.tw at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Wednesday, July 31, 2013 6:58 PM
Subject: Re: [R] merge matrix row data



Dear Arun, 

Thank you for the clear explanation.
The row.names question is a mistyping, for I do not have enough sleep last night.

Two more questions

1. If the row names are 1, 2, and 4 etc (numbers) instead of GID 1, GID 2, and GID 3, 
   is there any modification in need for the code ?

2. Please kindly explain the code
    (!!colSums(x1))*1}

   It is the critical part to merge the row data.

Thanks again.

Elaine



On Thu, Aug 1, 2013 at 6:45 AM, arun <smartpink111 at yahoo.com> wrote:

Dear Elaine,
>
>I used that line only because you didn't provide the data using dput().  So, I need to either use delimiter  "," or just leave a "space" by first joining the "GID" and the "numbers" using "_".  I chose the latter as I didn't had that much time to spent by putting "," between each entries.  After that, I removed "_" using the ?gsub().  As Bert pointed out, there are many online resources for understanding regular expression.
>
>In this particular case, what I did was to single out the "_" in the first pair of quotes, and replace with  space in the second pair of quotes " ".  Therefore, "GID_1", would become "GID 1", which is what your original dataset looks like.
>
>If you type row.names(mat1) on the R console and enter, you will be able to get the output. 
>
>Hope it helps.
>Arun
>
>
>
>
>
>
>
>
>________________________________
>From: Elaine Kuo <elaine.kuo.tw at gmail.com>
>To: arun <smartpink111 at yahoo.com>
>Cc: R help <r-help at r-project.org>
>Sent: Wednesday, July 31, 2013 5:07 PM
>Subject: Re: [R] merge matrix row data
>
>
>
>
>Dear Arun
>
>Thank you for the very useful help.
>However, please kindly explain the code below.
>row.names(mat1)<- gsub("[_]"," ",row.names(mat1))
>
>
>1. what does "[_]" mean?
>2. what does " "  mean?
>3. what does row.names(mat1) mean?
>
>I checked ?gsub but still did not get the idea.
>
>Thank you again
>
>Elaine
>
>
>
>On Wed, Jul 31, 2013 at 9:35 PM, arun <smartpink111 at yahoo.com> wrote:
>
>HI,
>>
>>Please use ?dput()
>>mat1<- as.matrix(read.table(text="
>>
>>D0989  D9820  D5629  D4327  D2134
>>GID_1    1        0        0      1      0
>>GID_2    0        1        1      0      0
>>GID_4    0        0        1      0      0
>>GID_5    1        1        0      0      0
>>GID_7    0        1        0      0      1
>>",sep="",header=TRUE))
>>row.names(mat1)<- gsub("[_]"," ",row.names(mat1))
>>IslandA<-c("GID 1", "GID 5")
>>IslandB<- c("GID 2", "GID 4", "GID 7")
>> res<-  t(sapply(c("IslandA","IslandB"),function(x) {x1<-mat1[match(get(x),row.names(mat1)),];(!!colSums(x1))*1} ))
>>
>> res
>>#        D0989 D9820 D5629 D4327 D2134
>>#IslandA     1     1     0     1     0
>>#IslandB     0     1     1     0     1
>>A.K.
>>
>>
>>
>>
>>
>>----- Original Message -----
>>From: Elaine Kuo <elaine.kuo.tw at gmail.com>
>>To: "r-help at stat.math.ethz.ch" <r-help at stat.math.ethz.ch>
>>Cc:
>>Sent: Wednesday, July 31, 2013 9:03 AM
>>Subject: [R] merge matrix row data
>>
>>Dear list,
>>
>>
>>
>>I have a matrix showing the species presence-absence on a map.
>>
>>Its rows are map locations, represented by GridCellID, such as GID1 and GID
>>5.
>>
>>Its columns are species ID, such as D0989, D9820, and D5629.
>>
>>The matrix is as followed.
>>
>>
>>
>>Now I want to merge the GridCellID according to the map location of each
>>island.
>>
>>For instance, Island A consist of GID 1 and 5. Island B consist of GID 2,
>>4, and 7.
>>
>>In GID 1 and 5, species D0989 are both 1.
>>
>>Then I want to merge GID 1 and 5 into Island A, with species D0989 as 1.
>>
>>The original matrix and the resulting matrix are listed below.
>>
>>Please kindly advise how to code the calculation in R.
>>
>>Please do not hesitate to ask if anything is unclear.
>>
>>Thank you in advance.
>>
>>
>>
>>Elaine
>>
>>
>>
>>Original matrix
>>
>>        D0989   D9820  D5629  D4327  D2134
>>
>>GID 1    1        0        0       1      0
>>
>>GID 2    0        1        1       0      0
>>
>>GID 4    0        0        1       0      0
>>
>>GID 5    1        1        0       0      0
>>
>>GID 7    0        1        0       0      1
>>
>>
>>
>>Resulting matrix
>>
>>                D0989   D9820  D5629  D4327  D2134
>>
>>Island A   1        1       0       1       0
>>
>>Island B   0        1       1       0       1
>>
>>    [[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.
>>
>>
>      



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