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Elaine Kuo

2013-Jul-31 13:03 UTC

[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]]

arun

2013-Jul-31 13:35 UTC

head link

[R] merge matrix row data

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.

arun

2013-Jul-31 23:15 UTC

head link

[R] merge matrix row data

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.
>>
>>
>? ????

arun

2013-Aug-01 12:08 UTC

head link

[R] merge matrix row data

mat1<-structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 
13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 
1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 
1L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L), .Dim = c(20L, 
14L), .Dimnames = list(NULL, c("GID", "D0407",
"D0409", "D0410",
"D0462", "D0463", "D0473", "D0475",
"D0488", "D0489", "D0492",
"D0493", "D0504", "D0536")))

IslandA<-c("GID 1", "GID 5")
IslandB<- c("GID 2", "GID 4", "GID 7")
t(sapply(c("IslandA","IslandB"),function(x) {x1<-
mat1[match(gsub(".*\\s+","",get(x)),mat1[,1]),-1];(!!colSums(x1))*1}))

?# ???? D0407 D0409 D0410 D0462 D0463 D0473 D0475 D0488 D0489 D0492 D0493 D0504
#IslandA???? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 0
#IslandB???? 0???? 0???? 0???? 0???? 0???? 1???? 0???? 0???? 0???? 0???? 1???? 0
?# ????? D0536
#IslandA???? 0
#IslandB???? 1
A.K.





________________________________
From: Elaine Kuo <elaine.kuo.tw at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Thursday, August 1, 2013 7:57 AM
Subject: Re: [R] merge matrix row data



Thanks.

Here you go.

structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L,?
13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L,?
1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L,?
1L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L), .Dim = c(20L,?
14L), .Dimnames = list(NULL, c("GID", "D0407",
"D0409", "D0410",?
"D0462", "D0463", "D0473", "D0475",
"D0488", "D0489", "D0492",?
"D0493", "D0504", "D0536")))

arun

2013-Aug-01 15:18 UTC

head link

[R] merge matrix row data

HI Elaine,
From the error, it looks like there are cases where none of the elements in one
of the element matches to the GID column of dataNP.m.
It's only a guess as you didn't provide? information about the
"Islands".

I was able to recreate the error you got.
dataNP.m<-structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 
13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 
1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 
1L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L), .Dim = c(20L, 
14L), .Dimnames = list(NULL, c("GID", "D0407",
"D0409", "D0410",
"D0462", "D0463", "D0473", "D0475",
"D0488", "D0489", "D0492",
"D0493", "D0504", "D0536")))

Conti_Australia<- c(1,14,18)
Conti_Malay<- c(2,6,8)
Island_Sumatra<- c(3,9,21)
Island_New_Guinea<- c(22,24,28) #none of the elements are present in the GID
column of example dataset
lapply(c("Conti_Australia","Conti_Malay","Island_Sumatra","Island_New_Guinea"),function(x)
{x1<- match(get(x),dataNP.m[,1]); x2<-x1[!is.na(x1)];colSums(x2)})
#Error in colSums(x2) : 'x' must be an array of at least two dimensions


lst1<-sapply(c("Conti_Australia","Conti_Malay","Island_Sumatra","Island_New_Guinea"),function(x)
{x1<- match(get(x),dataNP.m[,1]); x2<-x1[!is.na(x1)];if(length(x2)>0)
(!!colSums(dataNP.m[x2,-1]))*1})

t(simplify2array(lst1[lapply(lst1,length)>0]))
#??????????????? D0407 D0409 D0410 D0462 D0463 D0473 D0475 D0488 D0489 D0492
#Conti_Australia???? 0???? 0???? 0???? 0???? 0???? 1???? 0???? 0???? 0???? 0
#Conti_Malay???????? 0???? 0???? 0???? 0???? 0???? 1???? 0???? 0???? 0???? 0
#Island_Sumatra????? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 1
#??????????????? D0493 D0504 D0536
#Conti_Australia???? 0???? 0???? 1
#Conti_Malay???????? 1???? 0???? 1
#Island_Sumatra????? 0???? 0???? 0

A.K.





________________________________
From: Elaine Kuo <elaine.kuo.tw at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Thursday, August 1, 2013 9:20 AM
Subject: Re: [R] merge matrix row data



Hello arun,?

It is Elaine again.

After running the function in the last sentence of your code,?
an error message says
Error in colSums(x1) : 'x' must be an array of at least two dimensions


Please kindly help and thanks

Elaine

dput
> dput(head(dataNP.m,20))structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L,?
13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L,?
1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L,?
1L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L), .Dim = c(20L,?
14L), .Dimnames = list(NULL, c("GID", "D0407",
"D0409", "D0410",?
"D0462", "D0463", "D0473", "D0475",
"D0488", "D0489", "D0492",?
"D0493", "D0504", "D0536")))

Code

?island<- t(sapply(c(
"Conti_Australia","Conti_Korea","Conti_Malay",
+ ? ? ? ? ? ? ? ? ?
?"Island_Sumatra","Island_Bali","Island_Lombok",
+ ? ? ? ? ? ? ? ? ?
?"Island_Lesser_Sunda","Island_Maluku","Island_Sulawesi","Island_Kepu_Sula",
+ ? ? ? ? ? ? ? ? ?
?"Island_New_Guinea","Island_Palawan","Island_Phillipines",
+ ? ? ? ? ? ? ? ? ? ?"Island_Hainan","Island_Taiwan",
+ ? ? ? ? ? ? ? ? ?
?"Island_Sakishima","Island_Ryukyu","Island_Amami","Island_Osumi",
+ ? ? ? ? ? ? ? ? ?
?"Island_Kyushu","Island_Shikoku","Island_Honshu","Island_Hokkaido","Island_Sakhalin"),
+ ?function(x) {x1<-
dataNP.m[match(get(x),dataNP.m[,1]),-1];(!!colSums(x1))*1}))?




On Thu, Aug 1, 2013 at 8:41 PM, arun <smartpink111 at yahoo.com> wrote:

Hi Elaine,>No problem.
>Regards,
>
>Arun
>
>
>
>
>
>________________________________
>From: Elaine Kuo <elaine.kuo.tw at gmail.com>
>To: arun <smartpink111 at yahoo.com>
>Sent: Thursday, August 1, 2013 8:40 AM
>
>Subject: Re: [R] merge matrix row data
>
>
>
>Yes, you are right. Now it is time to compare GID value and islands.
>It worked well. :P
>Thanks Arun very much.
>You made my work finish much earlier than I expected
>
>Have a nice day
>
>Elaine
>
>
>
>On Thu, Aug 1, 2013 at 8:34 PM, arun <smartpink111 at yahoo.com>
wrote:
>
>Currently, I am really confused as to how your data looks like.
>>You showed me some data and I was able to process it.? Now, what is with
the row.names.? We are not comparing the row.names anymore.? Isn't the
comparison between the GID column and the values in Islands?
>>Also, it is difficult to pinpoint just by looking at that piece of
code.? There are no errors or anything.? It would be better if you tell me
exactly what the problem is..
>>
>>
>>
>>
>>
>>
>>
>>________________________________
>>From: Elaine Kuo <elaine.kuo.tw at gmail.com>
>>To: arun <smartpink111 at yahoo.com>
>>Sent: Thursday, August 1, 2013 8:30 AM
>>
>>Subject: Re: [R] merge matrix row data
>>
>>
>>
>>Hello Arun,?
>>
>>Thanks.
>>
>>However, the problem is that row.names cannot be read once it turns to
be 1, 2, 3 instead of GID 1, GID 2, GID 3.
>>Therefore, it is not possible to copy value from GID to islands.
>>
>>Please kindly help indicate where the error could be. (response: NULL)
>>Thanks..
>>
>>Code
>>?dataNP_1
<-read.dbf("H:/temp_D/stage_4_R_2748_S/NP_1067/Anseriformes_13.dbf",
as.is = FALSE)
>>dataNP.m<- as.matrix(dataNP_1,header=TRUE)
>>row.names(dataNP.m)
>>
>>
>>
>>
>>On Thu, Aug 1, 2013 at 8:24 PM, arun <smartpink111 at yahoo.com>
wrote:
>>
>>HI Elaine,
>>>
>>>So, according to your new post, it seems like:
>>>IslandA<- c("1","5")
>>>IslandB<- c("2","4","7")
>>>In that case, you don't need the gsub()
>>>
>>>
>>>?t(sapply(c("IslandA","IslandB"),function(x)
{x1<- mat1[match(get(x),mat1[,1]),-1];(!!colSums(x1))*1}))
>>>#??????? D0407 D0409 D0410 D0462 D0463 D0473 D0475 D0488 D0489 D0492
D0493 D0504
>>>
>>>#IslandA???? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 0????
0???? 0???? 0
>>>#IslandB???? 0???? 0???? 0???? 0???? 0???? 1???? 0???? 0???? 0????
0???? 1???? 0
>>>#??????? D0536
>>>#IslandA???? 0
>>>#IslandB???? 1
>>>
>>>
>>>Also, Inline:
>>>
>>>
>>>
>>>
>>>________________________________
>>>From: Elaine Kuo <elaine.kuo.tw at gmail.com>
>>>To: arun <smartpink111 at yahoo.com>
>>>Sent: Thursday, August 1, 2013 8:17 AM
>>>
>>>Subject: Re: [R] merge matrix row data
>>>
>>>
>>>
>>>
>>>Let's solve the questions one ?by one.
>>>
>>>1.?In the second row of the first column, it used to be GID 1 in the
first e-mail. "
>>>Are you saying that first column is "GID",
"GID", "GID", and 2nd column is 1, 2, 4 etc?
>>>
>>>=> No. The first column is GID, 1, 2, 3, .....But the first row
of the first column is GID (column name.)
>>>
>>>
>>>2. This dput() is also not full (so can't be used). Trying
subset a smaller dataset and dput that subset.
>>>=> No. This is a full set of data. I chose a genus with 13
species (Dxxxx).
>>>
>>>
>>>Let it be.? if the output of dput() is not complete, it can be
used.? That is the reason I asked for dput(head(dataset,20)) so that it gets the
first 20 rows of data.
>>>
>>>
>>>
>>>? ? ?Please kindly forget the example in previous e-mails.
>>>
>>>3.?Are they of the same format as below?
>>>
>>>
>>>
>>>IslandA<-c("GID 1", "GID 5")
>>>IslandB<- c("GID 2", "GID 4", "GID
7")
>>>
>>>=> Actually the GID range from 1 to 4873.
>>>? ? IslandA and IslandB are example for actual islands.?
>>>? ? Please forget Island A and B and let's go into the real
world.?
>>>? ?Here are some actual islands I just finished compiling.
>>>
>>>? ?Island_Bali<-c("971","972")?
>>>? ?Island_Lombok<-c("973","946")?
>>>? Island_Kepu_Sula<-c("1163","1164")?
>>>
>>>
>>>
>>>
>>>A.K.
>>>
>>>
>>>
>>>On Thu, Aug 1, 2013 at 8:01 PM, arun <smartpink111 at
yahoo.com> wrote:
>>>
>>>Also, here the GID numbers are from 1 to 20.? What is the
corresponding GID's in IslandA and IslandB?? Is it the same as you posted
previously?
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>________________________________
>>>> From: Elaine Kuo <elaine.kuo.tw at gmail.com>
>>>>To: arun <smartpink111 at yahoo.com>
>>>>Sent: Thursday, August 1, 2013 7:57 AM
>>>>
>>>>Subject: Re: [R] merge matrix row data
>>>>
>>>>
>>>>
>>>>Thanks.
>>>>
>>>>
>>>>Here you go.
>>>>
>>>>
>>>>structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L,?
>>>>13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 0L, 0L, 0L, 0L, 0L, 0L,?
>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>>>>0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L,?
>>>>1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>>>>1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>>>>0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L,?
>>>>1L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L), .Dim =
c(20L,?
>>>>14L), .Dimnames = list(NULL, c("GID",
"D0407", "D0409", "D0410",?
>>>>"D0462", "D0463", "D0473",
"D0475", "D0488", "D0489", "D0492",?
>>>>"D0493", "D0504", "D0536")))
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>On Thu, Aug 1, 2013 at 7:55 PM, arun <smartpink111 at
yahoo.com> wrote:
>>>>
>>>>HI Elaine,
>>>>>It seems like you skippped a part of the dput() output.?
Without the full, it is not useful.? Try copy and paste the output you showed in
your R console.? I am not asking for the full data to be dput().? Just
>>>>>dput(head(dataset,20))
>>>>>
>>>>>
>>>>>A.K.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>________________________________
>>>>>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: Thursday, August 1, 2013 5:25 AM
>>>>>
>>>>>Subject: Re: [R] merge matrix row data
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>Hello arun
>>>>>I modified your
>>>>>code a little bit but failed to retrieve the row.names.
>>>>>The response is
>>>>>NULL.
>>>>>Please kindly help
>>>>>and thanks.
>>>>>Elaine?
>>>>>
>>>>>Code
>>>>>load("h:/b_W_line/R_workspace/dataset_Residence_2748.RData")
>>>>>? dim(dataR)
>>>>>? str(dataR)
>>>>>? dataR.m<- as.matrix(dataR, header=TRUE)
>>>>>? dataR.m[,1]?
>>>>>? row.names(dataR.m)
>>>>>
>>>>>dput(dataR.m)
>>>>>.skipped...0L,
>>>>>0L, 0L, 0L,
>>>>>0L, 0L, 0L,
>>>>>0L, 0L, 0L,
>>>>>0L, 0L,
>>>>>0L, 0L, 0L),
>>>>>.Dim = c(4873L, 14L), .Dimnames = list(NULL,
>>>>>??? c("GID", "D0407",
>>>>>"D0409", "D0410", "D0462",
"D0463",
>>>>>"D0473",
>>>>>??? "D0475",
>>>>>"D0488", "D0489", "D0492",
"D0493",
>>>>>"D0504", "D0536"
>>>>>
>>>>>)))
>>>>>
>>>>>
>>>>>
>>>>>On Thu, Aug 1, 2013 at 1:24 PM, Elaine Kuo <elaine.kuo.tw
at gmail.com> wrote:
>>>>>
>>>>>Hello Arun
>>>>>>
>>>>>>
>>>>>>Thank for comments.
>>>>>>
>>>>>>
>>>>>>You are right. GID is?the first column in the matrix
this time.
>>>>>>
>>>>>>
>>>>>>In the second row of the first column, it used to be GID
1 in the first e-mail.
>>>>>>But you are also right. You answered it already, and
?this time?In the second row of the first column is 1.
>>>>>>Below is part of dput()(too many columns)
>>>>>>
>>>>>>
>>>>>>...... .Names = c("GID",?
>>>>>>"D5291", "D5293", "D7414",
"D7415", "D7416", "D7417", "D7418",?
>>>>>>"D7419", "D7420", "D7421",
"D7422", "D7423", "D7424", "D7425",?
>>>>>>"D7426", "D7427", "D7428",
"D7429", "D7430", "D7431", "D7432",?
>>>>>>"D7433", "D7434", "D7435",
"D7436", "D7437", "D7438", "D7439",?
>>>>>>"D7440", "D7441", "D7442",
"D7443", "D7444", "D7445", "D7446",?
>>>>>>"Elaine
>>>>>>
>>>>>>
>>>>>>
>>>>>>On Thu, Aug 1, 2013 at 12:35 PM, arun <smartpink111
at yahoo.com> wrote:
>>>>>>
>>>>>>
>>>>>>>
>>>>>>>Hi Elaine,
>>>>>>>I am not sure how your "original matrix"
keeps on changing from the original post.? Here, your statement about rownames
are 1, 2, 4 (the answer I already provided in the last post) and the matrix you
showed looks different.? It seems like GID is the first column in the matrix.? I
requested you to dput() the data to reduce these confusions.
>>>>>>>
>>>>>>>mat1<-as.matrix(read.table(text="
>>>>>>>
>>>>>>>GID?????? 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
>>>>>>>",sep="",header=TRUE))
>>>>>>>
>>>>>>>IslandA<-c("GID 1", "GID 5")
>>>>>>>IslandB<- c("GID 2", "GID 4",
"GID
7")t(sapply(c("IslandA","IslandB"),function(x) {x1<-
mat1[match(gsub(".*\\s+","",get(x)),mat1[,1]),-1];(!!colSums(x1))*1}))
>>>>>>>
>>>>>>>#??????? D0989 D9820 D5629 D4327 D2134
>>>>>>>
>>>>>>>#IslandA???? 1???? 1???? 0???? 1???? 0
>>>>>>>#IslandB???? 0???? 1???? 1???? 0???? 1
>>>>>>>A.K.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>________________________________
>>>>>>>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: Thursday, August 1, 2013 12:00 AM
>>>>>>>
>>>>>>>Subject: Re: [R] merge matrix row data
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>Hello arun
>>>>>>>
>>>>>>>Thanks for the answers.
>>>>>>>I understand the answer to question 2.
>>>>>>>However, about question 1, sorry I did not clarify
the question.
>>>>>>>
>>>>>>>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 ?
>>>>>>>? ?The original data looks like below.
>>>>>>>
>>>>>>>Original matrix
>>>>>>>GID ? ? ? 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
>>>>>>>
>>>>>>>Resulting matrix
>>>>>>>????????????????D0989?? D9820? D5629? D4327? D2134
>>>>>>>Island A?? 1??????? 1?????? 0?????? 1?????? 0
>>>>>>>Island B?? 0??????? 1?????? 1?????? 0?????? 1
>>>>>>>
>>>>>>>Elaine
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>On Thu, Aug 1, 2013 at 7:15 AM, arun
<smartpink111 at yahoo.com> wrote:
>>>>>>>
>>>>>>>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.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>? ????
>>>>>>>>?
>>>>>>>
>>>>>>???
>>>>>
>>>>
>>>>
>>>>
>>>
>>
>

arun

2013-Aug-02 02:48 UTC

head link

[R] merge matrix row data

Hi Elaine,

I didn't find any errors by running the code.
Regarding the first question, the former is of class "numeric", and
latter is "character"
library(foreign)
dataNP_1 <-read.dbf("Anseriformes_13.dbf", as.is = FALSE)
##all the other vectors


res<-t(sapply(c(
"Conti_Australia","Conti_Korea","Conti_Malay",
??????????????????
"Island_Sumatra","Island_Bali","Island_Lombok",
??????????????????
"Island_Lesser_Sunda","Island_Maluku","Island_Sulawesi","Island_Kepu_Sula",
??????????????????
"Island_New_Guinea","Island_Palawan","Island_Phillipines",
?????????????????? "Island_Hainan","Island_Taiwan", 
??????????????????
"Island_Sakishima","Island_Ryukyu","Island_Amami","Island_Osumi",
??????????????????
"Island_Kyushu","Island_Shikoku","Island_Honshu","Island_Hokkaido","Island_Sakhalin"),
?function(x) {x1<-
match(get(x),dataNP_1[,1]);(!!colSums(dataNP_1[x1,-1]))*1}))
head(res,3)
#??????????????? D0407 D0409 D0410 D0462 D0463 D0473 D0475 D0488 D0489 D0492
#Conti_Australia???? 0???? 0???? 1???? 0???? 0???? 0???? 0???? 0???? 0???? 0
#Conti_Korea???????? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 0
#Conti_Malay???????? 0???? 0???? 0???? 1???? 0???? 0???? 0???? 0???? 0???? 0
?# ????????????? D0493 D0504 D0536
#Conti_Australia???? 0???? 0???? 0
#Conti_Korea???????? 0???? 0???? 0
#Conti_Malay???????? 0???? 0???? 0


A.K.



________________________________
From: Elaine Kuo <elaine.kuo.tw at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Thursday, August 1, 2013 6:37 PM
Subject: Re: [R] merge matrix row data



Hello Arun,?

Thanks. I went to bed early and did not reply to your mail immediately.
I have some questions.

1. What is the difference between?Conti_Australia<- c(1,14,18)
and??Conti_Australia<- c("1","14","18")
? ?Both generated the same error message:?
? ? Error in colSums(x1) : 'x' must be an array of at least two
dimensions

2. I used your following code but found nothing NULL.
?
?lapply(c("Conti_Australia","Conti_Korea","Conti_Malay",
???????????????????
"Island_Sumatra","Island_Bali","Island_Lombok",

???????????????????
"Island_Lesser_Sunda","Island_Maluku","Island_Sulawesi","Island_Kepu_Sula",

???????????????????
"Island_New_Guinea","Island_Palawan","Island_Phillipines",
??????????????????? "Island_Hainan","Island_Taiwan",

???????????????????
"Island_Sakishima","Island_Ryukyu","Island_Amami","Island_Osumi",

???????????????????
"Island_Kyushu","Island_Shikoku","Island_Honshu","Island_Hokkaido","Island_Sakhalin"),
? function(x) {x1<- dataNP.m[match(get(x),dataNP.m[,1]),-1]})

3. I attached the data of Anseriformes and code of islands for your reference.
? ? Thanks.

Elaine





On Thu, Aug 1, 2013 at 11:19 PM, arun <smartpink111 at yahoo.com> wrote:

>
>A typo:
>
>none of the elements in one of the element
>should be read as:
>none of the elements in one of the "Islands"
>
>
>
>----- Original Message -----
>From: arun <smartpink111 at yahoo.com>
>To: Elaine Kuo <elaine.kuo.tw at gmail.com>
>
>Cc: R help <r-help at r-project.org>
>Sent: Thursday, August 1, 2013 11:18 AM
>Subject: Re: [R] merge matrix row data
>
>HI Elaine,
>From the error, it looks like there are cases where none of the elements in
one of the element matches to the GID column of dataNP.m.
>It's only a guess as you didn't provide? information about the
"Islands".
>
>I was able to recreate the error you got.
>dataNP.m<-structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L,
>13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 0L, 0L, 0L, 0L, 0L, 0L,
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
>0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L,
>1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
>1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
>0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L,
>1L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L), .Dim = c(20L,
>14L), .Dimnames = list(NULL, c("GID", "D0407",
"D0409", "D0410",
>"D0462", "D0463", "D0473", "D0475",
"D0488", "D0489", "D0492",
>"D0493", "D0504", "D0536")))
>
>Conti_Australia<- c(1,14,18)
>Conti_Malay<- c(2,6,8)
>Island_Sumatra<- c(3,9,21)
>Island_New_Guinea<- c(22,24,28) #none of the elements are present in the
GID column of example dataset
>lapply(c("Conti_Australia","Conti_Malay","Island_Sumatra","Island_New_Guinea"),function(x)
{x1<- match(get(x),dataNP.m[,1]); x2<-x1[!is.na(x1)];colSums(x2)})
>#Error in colSums(x2) : 'x' must be an array of at least two
dimensions
>
>
>lst1<-sapply(c("Conti_Australia","Conti_Malay","Island_Sumatra","Island_New_Guinea"),function(x)
{x1<- match(get(x),dataNP.m[,1]); x2<-x1[!is.na(x1)];if(length(x2)>0)
(!!colSums(dataNP.m[x2,-1]))*1})
>
>t(simplify2array(lst1[lapply(lst1,length)>0]))
>#??????????????? D0407 D0409 D0410 D0462 D0463 D0473 D0475 D0488 D0489 D0492
>#Conti_Australia???? 0???? 0???? 0???? 0???? 0???? 1???? 0???? 0???? 0???? 0
>#Conti_Malay???????? 0???? 0???? 0???? 0???? 0???? 1???? 0???? 0???? 0???? 0
>#Island_Sumatra????? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 1
>#??????????????? D0493 D0504 D0536
>#Conti_Australia???? 0???? 0???? 1
>#Conti_Malay???????? 1???? 0???? 1
>#Island_Sumatra????? 0???? 0???? 0
>
>A.K.
>
>
>
>
>
>________________________________
>From: Elaine Kuo <elaine.kuo.tw at gmail.com>
>To: arun <smartpink111 at yahoo.com>
>Sent: Thursday, August 1, 2013 9:20 AM
>Subject: Re: [R] merge matrix row data
>
>
>
>Hello arun,?
>
>It is Elaine again.
>
>After running the function in the last sentence of your code,?
>an error message says
>Error in colSums(x1) : 'x' must be an array of at least two
dimensions
>
>
>Please kindly help and thanks
>
>Elaine
>
>dput
>
>> dput(head(dataNP.m,20))
>structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L,?
>13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 0L, 0L, 0L, 0L, 0L, 0L,?
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L,?
>1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,?
>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L,?
>1L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L), .Dim = c(20L,?
>14L), .Dimnames = list(NULL, c("GID", "D0407",
"D0409", "D0410",?
>"D0462", "D0463", "D0473", "D0475",
"D0488", "D0489", "D0492",?
>"D0493", "D0504", "D0536")))
>
>Code
>
>?island<- t(sapply(c(
"Conti_Australia","Conti_Korea","Conti_Malay",
>+ ? ? ? ? ? ? ? ? ?
?"Island_Sumatra","Island_Bali","Island_Lombok",
>+ ? ? ? ? ? ? ? ? ?
?"Island_Lesser_Sunda","Island_Maluku","Island_Sulawesi","Island_Kepu_Sula",
>+ ? ? ? ? ? ? ? ? ?
?"Island_New_Guinea","Island_Palawan","Island_Phillipines",
>+ ? ? ? ? ? ? ? ? ? ?"Island_Hainan","Island_Taiwan",
>+ ? ? ? ? ? ? ? ? ?
?"Island_Sakishima","Island_Ryukyu","Island_Amami","Island_Osumi",
>+ ? ? ? ? ? ? ? ? ?
?"Island_Kyushu","Island_Shikoku","Island_Honshu","Island_Hokkaido","Island_Sakhalin"),
>+ ?function(x) {x1<-
dataNP.m[match(get(x),dataNP.m[,1]),-1];(!!colSums(x1))*1}))?
>
>
>
>
>On Thu, Aug 1, 2013 at 8:41 PM, arun <smartpink111 at yahoo.com>
wrote:
>
>Hi Elaine,
>>No problem.
>>Regards,
>>
>>Arun
>>
>>
>>
>>
>>
>>________________________________
>>From: Elaine Kuo <elaine.kuo.tw at gmail.com>
>>To: arun <smartpink111 at yahoo.com>
>>Sent: Thursday, August 1, 2013 8:40 AM
>>
>>Subject: Re: [R] merge matrix row data
>>
>>
>>
>>Yes, you are right. Now it is time to compare GID value and islands.
>>It worked well. :P
>>Thanks Arun very much.
>>You made my work finish much earlier than I expected
>>
>>Have a nice day
>>
>>Elaine
>>
>>
>>
>>On Thu, Aug 1, 2013 at 8:34 PM, arun <smartpink111 at yahoo.com>
wrote:
>>
>>Currently, I am really confused as to how your data looks like.
>>>You showed me some data and I was able to process it.? Now, what is
with the row.names.? We are not comparing the row.names anymore.? Isn't the
comparison between the GID column and the values in Islands?
>>>Also, it is difficult to pinpoint just by looking at that piece of
code.? There are no errors or anything.? It would be better if you tell me
exactly what the problem is..
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>________________________________
>>>From: Elaine Kuo <elaine.kuo.tw at gmail.com>
>>>To: arun <smartpink111 at yahoo.com>
>>>Sent: Thursday, August 1, 2013 8:30 AM
>>>
>>>Subject: Re: [R] merge matrix row data
>>>
>>>
>>>
>>>Hello Arun,?
>>>
>>>Thanks.
>>>
>>>However, the problem is that row.names cannot be read once it turns
to be 1, 2, 3 instead of GID 1, GID 2, GID 3.
>>>Therefore, it is not possible to copy value from GID to islands.
>>>
>>>Please kindly help indicate where the error could be. (response:
NULL)
>>>Thanks..
>>>
>>>Code
>>>?dataNP_1
<-read.dbf("H:/temp_D/stage_4_R_2748_S/NP_1067/Anseriformes_13.dbf",
as.is = FALSE)
>>>dataNP.m<- as.matrix(dataNP_1,header=TRUE)
>>>row.names(dataNP.m)
>>>
>>>
>>>
>>>
>>>On Thu, Aug 1, 2013 at 8:24 PM, arun <smartpink111 at
yahoo.com> wrote:
>>>
>>>HI Elaine,
>>>>
>>>>So, according to your new post, it seems like:
>>>>IslandA<- c("1","5")
>>>>IslandB<- c("2","4","7")
>>>>In that case, you don't need the gsub()
>>>>
>>>>
>>>>?t(sapply(c("IslandA","IslandB"),function(x)
{x1<- mat1[match(get(x),mat1[,1]),-1];(!!colSums(x1))*1}))
>>>>#??????? D0407 D0409 D0410 D0462 D0463 D0473 D0475 D0488 D0489
D0492 D0493 D0504
>>>>
>>>>#IslandA???? 0???? 0???? 0???? 0???? 0???? 0???? 0???? 0????
0???? 0???? 0???? 0
>>>>#IslandB???? 0???? 0???? 0???? 0???? 0???? 1???? 0???? 0????
0???? 0???? 1???? 0
>>>>#??????? D0536
>>>>#IslandA???? 0
>>>>#IslandB???? 1
>>>>
>>>>
>>>>Also, Inline:
>>>>
>>>>
>>>>
>>>>
>>>>________________________________
>>>>From: Elaine Kuo <elaine.kuo.tw at gmail.com>
>>>>To: arun <smartpink111 at yahoo.com>
>>>>Sent: Thursday, August 1, 2013 8:17 AM
>>>>
>>>>Subject: Re: [R] merge matrix row data
>>>>
>>>>
>>>>
>>>>
>>>>Let's solve the questions one ?by one.
>>>>
>>>>1.?In the second row of the first column, it used to be GID 1 in
the first e-mail. "
>>>>Are you saying that first column is "GID",
"GID", "GID", and 2nd column is 1, 2, 4 etc?
>>>>
>>>>=> No. The first column is GID, 1, 2, 3, .....But the first
row of the first column is GID (column name.)
>>>>
>>>>
>>>>2. This dput() is also not full (so can't be used). Trying
subset a smaller dataset and dput that subset.
>>>>=> No. This is a full set of data. I chose a genus with 13
species (Dxxxx).
>>>>
>>>>
>>>>Let it be.? if the output of dput() is not complete, it can be
used.? That is the reason I asked for dput(head(dataset,20)) so that it gets the
first 20 rows of data.
>>>>
>>>>
>>>>
>>>>? ? ?Please kindly forget the example in previous e-mails.
>>>>
>>>>3.?Are they of the same format as below?
>>>>
>>>>
>>>>
>>>>IslandA<-c("GID 1", "GID 5")
>>>>IslandB<- c("GID 2", "GID 4", "GID
7")
>>>>
>>>>=> Actually the GID range from 1 to 4873.
>>>>? ? IslandA and IslandB are example for actual islands.?
>>>>? ? Please forget Island A and B and let's go into the real
world.?
>>>>? ?Here are some actual islands I just finished compiling.
>>>>
>>>>? ?Island_Bali<-c("971","972")?
>>>>? ?Island_Lombok<-c("973","946")?
>>>>? Island_Kepu_Sula<-c("1163","1164")?
>>>>
>>>>
>>>>
>>>>
>>>>A.K.
>>>>
>>>>
>>>>
>>>>On Thu, Aug 1, 2013 at 8:01 PM, arun <smartpink111 at
yahoo.com> wrote:
>>>>
>>>>Also, here the GID numbers are from 1 to 20.? What is the
corresponding GID's in IslandA and IslandB?? Is it the same as you posted
previously?
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>________________________________
>>>>> From: Elaine Kuo <elaine.kuo.tw at gmail.com>
>>>>>To: arun <smartpink111 at yahoo.com>
>>>>>Sent: Thursday, August 1, 2013 7:57 AM
>>>>>
>>>>>Subject: Re: [R] merge matrix row data
>>>>>
>>>>>
>>>>>
>>>>>Thanks.
>>>>>
>>>>>
>>>>>Here you go.
>>>>>
>>>>>
>>>>>structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L,
12L,?
>>>>>13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 0L, 0L, 0L, 0L, 0L,
0L,?
>>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L,?
>>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L,?
>>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L,?
>>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L,?
>>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L,?
>>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L,?
>>>>>0L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L,
1L,?
>>>>>1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L,?
>>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L,?
>>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L,?
>>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L,?
>>>>>1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L,?
>>>>>0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L,?
>>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L,?
>>>>>0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
1L,?
>>>>>1L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L),
.Dim = c(20L,?
>>>>>14L), .Dimnames = list(NULL, c("GID",
"D0407", "D0409", "D0410",?
>>>>>"D0462", "D0463", "D0473",
"D0475", "D0488", "D0489", "D0492",?
>>>>>"D0493", "D0504", "D0536")))
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>On Thu, Aug 1, 2013 at 7:55 PM, arun <smartpink111 at
yahoo.com> wrote:
>>>>>
>>>>>HI Elaine,
>>>>>>It seems like you skippped a part of the dput() output.?
Without the full, it is not useful.? Try copy and paste the output you showed in
your R console.? I am not asking for the full data to be dput().? Just
>>>>>>dput(head(dataset,20))
>>>>>>
>>>>>>
>>>>>>A.K.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>________________________________
>>>>>>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: Thursday, August 1, 2013 5:25 AM
>>>>>>
>>>>>>Subject: Re: [R] merge matrix row data
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>Hello arun
>>>>>>I modified your
>>>>>>code a little bit but failed to retrieve the row.names.
>>>>>>The response is
>>>>>>NULL.
>>>>>>Please kindly help
>>>>>>and thanks.
>>>>>>Elaine?
>>>>>>
>>>>>>Code
>>>>>>load("h:/b_W_line/R_workspace/dataset_Residence_2748.RData")
>>>>>>? dim(dataR)
>>>>>>? str(dataR)
>>>>>>? dataR.m<- as.matrix(dataR, header=TRUE)
>>>>>>? dataR.m[,1]?
>>>>>>? row.names(dataR.m)
>>>>>>
>>>>>>dput(dataR.m)
>>>>>>.skipped...0L,
>>>>>>0L, 0L, 0L,
>>>>>>0L, 0L, 0L,
>>>>>>0L, 0L, 0L,
>>>>>>0L, 0L,
>>>>>>0L, 0L, 0L),
>>>>>>.Dim = c(4873L, 14L), .Dimnames = list(NULL,
>>>>>>??? c("GID", "D0407",
>>>>>>"D0409", "D0410", "D0462",
"D0463",
>>>>>>"D0473",
>>>>>>??? "D0475",
>>>>>>"D0488", "D0489", "D0492",
"D0493",
>>>>>>"D0504", "D0536"
>>>>>>
>>>>>>)))
>>>>>>
>>>>>>
>>>>>>
>>>>>>On Thu, Aug 1, 2013 at 1:24 PM, Elaine Kuo
<elaine.kuo.tw at gmail.com> wrote:
>>>>>>
>>>>>>Hello Arun
>>>>>>>
>>>>>>>
>>>>>>>Thank for comments.
>>>>>>>
>>>>>>>
>>>>>>>You are right. GID is?the first column in the matrix
this time.
>>>>>>>
>>>>>>>
>>>>>>>In the second row of the first column, it used to be
GID 1 in the first e-mail.
>>>>>>>But you are also right. You answered it already, and
?this time?In the second row of the first column is 1.
>>>>>>>Below is part of dput()(too many columns)
>>>>>>>
>>>>>>>
>>>>>>>...... .Names = c("GID",?
>>>>>>>"D5291", "D5293",
"D7414", "D7415", "D7416", "D7417",
"D7418",?
>>>>>>>"D7419", "D7420",
"D7421", "D7422", "D7423", "D7424",
"D7425",?
>>>>>>>"D7426", "D7427",
"D7428", "D7429", "D7430", "D7431",
"D7432",?
>>>>>>>"D7433", "D7434",
"D7435", "D7436", "D7437", "D7438",
"D7439",?
>>>>>>>"D7440", "D7441",
"D7442", "D7443", "D7444", "D7445",
"D7446",?
>>>>>>>"Elaine
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>On Thu, Aug 1, 2013 at 12:35 PM, arun
<smartpink111 at yahoo.com> wrote:
>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>>Hi Elaine,
>>>>>>>>I am not sure how your "original
matrix" keeps on changing from the original post.? Here, your statement
about rownames are 1, 2, 4 (the answer I already provided in the last post) and
the matrix you showed looks different.? It seems like GID is the first column in
the matrix.? I requested you to dput() the data to reduce these confusions.
>>>>>>>>
>>>>>>>>mat1<-as.matrix(read.table(text="
>>>>>>>>
>>>>>>>>GID?????? 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
>>>>>>>>",sep="",header=TRUE))
>>>>>>>>
>>>>>>>>IslandA<-c("GID 1", "GID
5")
>>>>>>>>IslandB<- c("GID 2", "GID
4", "GID
7")t(sapply(c("IslandA","IslandB"),function(x) {x1<-
mat1[match(gsub(".*\\s+","",get(x)),mat1[,1]),-1];(!!colSums(x1))*1}))
>>>>>>>>
>>>>>>>>#??????? D0989 D9820 D5629 D4327 D2134
>>>>>>>>
>>>>>>>>#IslandA???? 1???? 1???? 0???? 1???? 0
>>>>>>>>#IslandB???? 0???? 1???? 1???? 0???? 1
>>>>>>>>A.K.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>________________________________
>>>>>>>>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: Thursday, August 1, 2013 12:00 AM
>>>>>>>>
>>>>>>>>Subject: Re: [R] merge matrix row data
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>Hello arun
>>>>>>>>
>>>>>>>>Thanks for the answers.
>>>>>>>>I understand the answer to question 2.
>>>>>>>>However, about question 1, sorry I did not
clarify the question.
>>>>>>>>
>>>>>>>>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 ?
>>>>>>>>? ?The original data looks like below.
>>>>>>>>
>>>>>>>>Original matrix
>>>>>>>>GID ? ? ? 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
>>>>>>>>
>>>>>>>>Resulting matrix
>>>>>>>>????????????????D0989?? D9820? D5629? D4327?
D2134
>>>>>>>>Island A?? 1??????? 1?????? 0?????? 1?????? 0
>>>>>>>>Island B?? 0??????? 1?????? 1?????? 0?????? 1
>>>>>>>>
>>>>>>>>Elaine
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>On Thu, Aug 1, 2013 at 7:15 AM, arun
<smartpink111 at yahoo.com> wrote:
>>>>>>>>
>>>>>>>>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.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>? ????
>>>>>>>>>?
>>>>>>>>
>>>>>>>???
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>

R help - Jul 2013 - merge matrix row data

[R] merge matrix row data

[R] merge matrix row data

[R] merge matrix row data

[R] merge matrix row data

[R] merge matrix row data

[R] merge matrix row data