Re: [R] problem with previous code
Excellent Arun, it worked, many thanks.
E.
On Thu, Mar 27, 2014 at 11:55 AM, arun wrote:
> HI Elio,
>
> May be this helps:
> indx <- order(gsub("\\d+","",colnames(res)))
> res1 <- res[indx,indx]
> A.K.
>
>
>
>
>
>
>
> On Thursday, March 27, 2014 6:24 AM, Elio Shijaku
> wrote:
>
> Hi Arun,
>
> Thanks a lot for your continuous help. I am attaching a sample with the
> row / column names. Basically, the order should be alphabetical because
> then I don´t need to rearrange the data in Excel and since I have many
> columns of data, the alphabetical order makes dealing with specific values
> easier since I can just copy the row where different variable values for
> the same name are located.
>
> Does this help answering your question?
>
> Best,
>
> E.
>
>
>
>
>
>
>
> >On Tuesday, March 25, 2014 3:57 PM, Elio Shijaku
> wrote:
> >
> >Hi Arun,
> >
> >Thanks a lot, it worked, one small question, is there any code to arrange
> the variables in each matrix in alphabetical order?
> >
> >Have a safe flight!
> >
> >
> >E.
> >
> >
> >
> >
> >On Tue, Mar 25, 2014 at 6:51 PM, arun wrote:
> >
> >HI Elio,
> >>I am at the airport. So, probably, I may not be able to access the
> emails that frequently.
> >>
> >>Arun
> >>
> >>
> >>
> >>On Tuesday, March 25, 2014 1:47 PM, arun wrote:
> >>Hi Elio,
> >>I gy.
> >>
> >>
> >>uess the error is here:
> >>
> >>
> >>as.vector(sapply(lst2,rownames)) #still a list
> >>
> >>length(unique(as.vector(sapply(lst2,rownames))) )# length of list
> >>
> >>#22
> >>
> >>
> >>uNrownames <- unique(unlist(sapply(lst2,rownames)))
> >> length(uNrownames)
> >>#[1] 90
> >>
> >>res <-
> matrix(0,nrow=length(uNrownames),ncol=length(uNrownames),dimnames=list(uNrownames,uNrownames))
> >>for(i in seq_along(lst2)){
> >> res[rownames(lst2[[i]]),rownames(lst2[[i]])] <-
> res[rownames(lst2[[i]]),rownames(lst2[[i]])]+lst2[[i]]
> >> res
> >> }
> >> dim(res)
> >>#[1] 90 90
> >> res[1:3,1:3]
> >># a15 a187 a200
> >>#a15011
> >>#a187 100
> >>#a200 100
> >>
> >>A.K.
> >>
> >>
> >>
> >>On Tuesday, March 25, 2014 12:50 PM, Elio Shijaku
> wrote:
> >>
> >>Hi Arun,
> >>
> >>Sorry to disturb once again but I have encountered an error while trying
> to combine 22 symmetric matrices of different dimensions (in the attached
> file) into one single symmetric matrix.
> >>
> >>Here is what I get as an error:
> >>
> >>
> >>> length(list.files(pattern=".txt")) [1] 22 > lst1 <-
> lapply(list.files(pattern=".txt"),function(x) +
> read.table(x,header=TRUE,stringsAsFactors=FALSE)) > sapply(lst1,dim) [,1]
> [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15]
> >>[1,] 65 68 63 72 70 72 73 78
> 77777580777576
> >>[2,] 65 68 63 72 70 72 73 78
> 77777580777576 [,16] [,17] [,18] [,19] [,20] [,21]
> [,22]
> >>[1,]77697366625956
> >>[2,]77697366625956 > sapply(lst1,function(x)
> all(apply(rbind(colnames(x),rownames(x)),2,function(y) y[1]==y[2]))) [1]
> TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> TRUE
> >>[17] TRUE TRUE TRUE TRUE TRUE TRUE > lst2 <- lapply(lst1,as.matrix) >
> uNrownames <- unique(as.vector(sapply(lst2,rownames))) > res <-
> matrix(0,nrow=length(uNrownames), ncol=length(uNrownames),
> dimnames=list(uNrownames,uNrownames)) > for(i in seq_along(lst2)){ +
> res[rownames(lst2[[i]]),rownames(lst2[[i]])] <-
> res[rownames(lst2[[i]]),rownames(lst2[[i]])] + lst2[[i]] + res + } Error in
> res[rownames(lst2[[i]]), rownames(lst2[[i]])] : subscript out of bounds
> >>
> >>
> >>Any idea about what may cause the error?
> >>
> >>Thanks a lot.
> >>
> >>Best,
> >>
> >>Elio
> >>
> >
>
[[alternative HTML version deleted]]
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Re: [R] problem with previous code
HI Elio,
May be this helps:
indx <- order(gsub("\\d+","",colnames(res)))
res1 <- res[indx,indx]
A.K.
On Thursday, March 27, 2014 6:24 AM, Elio Shijaku wrote:
Hi Arun,
Thanks a lot for your continuous help. I am attaching a sample with the row /
column names. Basically, the order should be alphabetical because then I don´t
need to rearrange the data in Excel and since I have many columns of data, the
alphabetical order makes dealing with specific values easier since I can just
copy the row where different variable values for the same name are located.
Does this help answering your question?
Best,
E.
>On Tuesday, March 25, 2014 3:57 PM, Elio Shijaku wrote:
>
>Hi Arun,
>
>Thanks a lot, it worked, one small question, is there any code to arrange the
>variables in each matrix in alphabetical order?
>
>Have a safe flight!
>
>
>E.
>
>
>
>
>On Tue, Mar 25, 2014 at 6:51 PM, arun wrote:
>
>HI Elio,
>>I am at the airport. So, probably, I may not be able to access the emails
>>that frequently.
>>
>>Arun
>>
>>
>>
>>On Tuesday, March 25, 2014 1:47 PM, arun wrote:
>>Hi Elio,
>>I gy.
>>
>>
>>uess the error is here:
>>
>>
>>as.vector(sapply(lst2,rownames)) #still a list
>>
>>length(unique(as.vector(sapply(lst2,rownames))) )# length of list
>>
>>#22
>>
>>
>>uNrownames <- unique(unlist(sapply(lst2,rownames)))
>> length(uNrownames)
>>#[1] 90
>>
>>res <-
>>matrix(0,nrow=length(uNrownames),ncol=length(uNrownames),dimnames=list(uNrownames,uNrownames))
>>for(i in seq_along(lst2)){
>> res[rownames(lst2[[i]]),rownames(lst2[[i]])] <-
>>res[rownames(lst2[[i]]),rownames(lst2[[i]])]+lst2[[i]]
>> res
>> }
>> dim(res)
>>#[1] 90 90
>> res[1:3,1:3]
>># a15 a187 a200
>>#a15 0 1 1
>>#a187 1 0 0
>>#a200 1 0 0
>>
>>A.K.
>>
>>
>>
>>On Tuesday, March 25, 2014 12:50 PM, Elio Shijaku wrote:
>>
>>Hi Arun,
>>
>>Sorry to disturb once again but I have encountered an error while trying to
>>combine 22 symmetric matrices of different dimensions (in the attached file)
>>into one single symmetric matrix.
>>
>>Here is what I get as an error:
>>
>>
>>> length(list.files(pattern=".txt")) [1] 22 > lst1 <-
>>> lapply(list.files(pattern=".txt"),function(x) +
>>> read.table(x,header=TRUE,stringsAsFactors=FALSE)) > sapply(lst1,dim) [,1]
>>> [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15]
>>[1,] 65 68 63 72 70 72 73 78 7777758077
>>7576
>>[2,] 65 68 63 72 70 72 73 78 7777758077
>>7576 [,16] [,17] [,18] [,19] [,20] [,21] [,22]
>>[1,]77697366625956
>>[2,]77697366625956 > sapply(lst1,function(x)
>>all(apply(rbind(colnames(x),rownames(x)),2,function(y) y[1]==y[2]))) [1]
>>TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
>>TRUE
>>[17] TRUE TRUE TRUE TRUE TRUE TRUE > lst2 <- lapply(lst1,as.matrix) >
>>uNrownames <- unique(as.vector(sapply(lst2,rownames))) > res <-
>>matrix(0,nrow=length(uNrownames), ncol=length(uNrownames),
>>dimnames=list(uNrownames,uNrownames)) > for(i in seq_along(lst2)){ +
>>res[rownames(lst2[[i]]),rownames(lst2[[i]])] <-
>>res[rownames(lst2[[i]]),rownames(lst2[[i]])] + lst2[[i]] + res + } Error in
>>res[rownames(lst2[[i]]), rownames(lst2[[i]])] : subscript out of bounds
>>
>>
>>Any idea about what may cause the error?
>>
>>Thanks a lot.
>>
>>Best,
>>
>>Elio
>>
>
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Re: [R] problem with previous code
Hi Elio,
I guess the error is here:
as.vector(sapply(lst2,rownames)) #still a list
length(unique(as.vector(sapply(lst2,rownames))) )# length of list
#22
uNrownames <- unique(unlist(sapply(lst2,rownames)))
length(uNrownames)
#[1] 90
res <-
matrix(0,nrow=length(uNrownames),ncol=length(uNrownames),dimnames=list(uNrownames,uNrownames))
for(i in seq_along(lst2)){
res[rownames(lst2[[i]]),rownames(lst2[[i]])] <-
res[rownames(lst2[[i]]),rownames(lst2[[i]])]+lst2[[i]]
res
}
dim(res)
#[1] 90 90
res[1:3,1:3]
# a15 a187 a200
#a15 0 1 1
#a187 1 0 0
#a200 1 0 0
A.K.
On Tuesday, March 25, 2014 12:50 PM, Elio Shijaku wrote:
Hi Arun,
Sorry to disturb once again but I have encountered an error while trying to
combine 22 symmetric matrices of different dimensions (in the attached file)
into one single symmetric matrix.
Here is what I get as an error:
> length(list.files(pattern=".txt")) [1] 22 > lst1 <-
> lapply(list.files(pattern=".txt"),function(x) +
> read.table(x,header=TRUE,stringsAsFactors=FALSE)) > sapply(lst1,dim) [,1]
> [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15]
[1,] 65 68 63 72 70 72 73 78 777775807775
76
[2,] 65 68 63 72 70 72 73 78 777775807775
76 [,16] [,17] [,18] [,19] [,20] [,21] [,22]
[1,]77697366625956
[2,]77697366625956 > sapply(lst1,function(x)
all(apply(rbind(colnames(x),rownames(x)),2,function(y) y[1]==y[2]))) [1] TRUE
TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[17] TRUE TRUE TRUE TRUE TRUE TRUE > lst2 <- lapply(lst1,as.matrix) >
uNrownames <- unique(as.vector(sapply(lst2,rownames))) > res <-
matrix(0,nrow=length(uNrownames), ncol=length(uNrownames),
dimnames=list(uNrownames,uNrownames)) > for(i in seq_along(lst2)){ +
res[rownames(lst2[[i]]),rownames(lst2[[i]])] <-
res[rownames(lst2[[i]]),rownames(lst2[[i]])] + lst2[[i]] + res + } Error in
res[rownames(lst2[[i]]), rownames(lst2[[i]])] : subscript out of bounds
Any idea about what may cause the error?
Thanks a lot.
Best,
Elio
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Re: [R] problem with previous code
Hi Arun,
Yes, that last command m1[indx2N] <- m2[sort(indx1)] did exactly the trick,
now the variable and their values are perfectly matched. Thanks a lot for
your great help.
Best,
Elio
On Wed, Mar 5, 2014 at 1:17 AM, arun wrote:
>
>
> Hi Elio,
>
> If you change the last line of the code:
>
> m1[indx2N] <- m2[indx1]
>
> to
> m1[indx2N] <- m2[sort(indx1)]
>
> sum(m1[rownames(m1)=="p79",])
> #[1] 191
> sum(m2[rownames(m2)=="p79",])
> #[1] 191
>
>
> The problem is in the order of the colnames/rownames in each of the
> datasets. I tested it on something like:
> m1 <- matrix(0,12,12,dimnames=rep(list(paste0("a",1:12)),2))
> set.seed(49)
> m2 <-
> matrix(sample(0:2,4*4,replace=TRUE),ncol=4,dimnames=rep(list(c("a4","a6","a9","a12")),2))
>
> which didn't show the problem.
>
>
> But, if I change the order of colnames:
>
> m1 <- matrix(0,12,12,dimnames=rep(list(paste0("a",c(1:3,8:12,4:7))),2))
>
> set.seed(49)
> m2 <-
> matrix(sample(0:2,4*4,replace=TRUE),ncol=4,dimnames=rep(list(c("a9","a4","a6","a12")),2))
> vec1 <- paste0(rownames(m1)[row(m1)],colnames(m1)[col(m1)])
> vec2 <- paste0(rownames(m2)[row(m2)],colnames(m2)[col(m2)])
> indx <- match(vec1,vec2)
> indx1 <- indx[!is.na(indx)]
>
> indx2 <- match(vec2,vec1)
> indx2N <- indx2[!is.na(indx2)]
> m1[indx2N] <- m2[sort(indx1)]
> m1
>
>
> Hope this helps.
> A.K.
>
>
>
>
>
>
> On Tuesday, March 4, 2014 3:16 PM, Elio Shijaku wrote:
>
> Hi Arun,
>
> Sorry to disturb, but while trying your code to combine two matrices of
> unequal dimensions, I noticed a problem, the sum for each variable does not
> match, but the overall variables sum does match for both matrices,
> something isn't going right, perhaps the variables are getting mixed up,
> any idea??
>
> Here is the code you sent me and the zipped files for testing:
>
>
> dat1 <-
> read.table("mtest.txt",header=TRUE)
> dim(dat1)
>
> dat2 <-
> read.table("1998res_x.txt",header=TRUE)
> dim(dat2)
> m1 <- as.matrix(dat1)
> m2 <- as.matrix(dat2)
> vec1 <-
> paste0(rownames(m1)[row(m1)],colnames(m1)[col(m1)])
> vec2 <- paste0(rownames(m2)[row(m2)],colnames(m2)[col(m2)])
> indx <- match(vec1,vec2)
> indx1 <- indx[!is.na(indx)]
> indx2 <- match(vec2,vec1)
> indx2N <- indx2[!is.na(indx2)]
> m1[indx2N] <- m2[indx1]
>
> Thanks a lot!!
>
>
> Best,
>
>
> Elio
>
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem with previous code
Hi Elio,
If you change the last line of the code:
m1[indx2N] <- m2[indx1]
to
m1[indx2N] <- m2[sort(indx1)]
sum(m1[rownames(m1)=="p79",])
#[1] 191
sum(m2[rownames(m2)=="p79",])
#[1] 191
The problem is in the order of the colnames/rownames in each of the datasets.
I tested it on something like:
m1 <- matrix(0,12,12,dimnames=rep(list(paste0("a",1:12)),2))
set.seed(49)
m2 <-
matrix(sample(0:2,4*4,replace=TRUE),ncol=4,dimnames=rep(list(c("a4","a6","a9","a12")),2))
which didn't show the problem.
But, if I change the order of colnames:
m1 <- matrix(0,12,12,dimnames=rep(list(paste0("a",c(1:3,8:12,4:7))),2))
set.seed(49)
m2 <-
matrix(sample(0:2,4*4,replace=TRUE),ncol=4,dimnames=rep(list(c("a9","a4","a6","a12")),2))
vec1 <- paste0(rownames(m1)[row(m1)],colnames(m1)[col(m1)])
vec2 <- paste0(rownames(m2)[row(m2)],colnames(m2)[col(m2)])
indx <- match(vec1,vec2)
indx1 <- indx[!is.na(indx)]
indx2 <- match(vec2,vec1)
indx2N <- indx2[!is.na(indx2)]
m1[indx2N] <- m2[sort(indx1)]
m1
Hope this helps.
A.K.
On Tuesday, March 4, 2014 3:16 PM, Elio Shijaku wrote:
Hi Arun,
Sorry to disturb, but while trying your code to combine two matrices of unequal
dimensions, I noticed a problem, the sum for each variable does not match, but
the overall variables sum does match for both matrices, something isn't going
right, perhaps the variables are getting mixed up, any idea??
Here is the code you sent me and the zipped files for testing:
dat1 <-
read.table("mtest.txt",header=TRUE)
dim(dat1)
dat2 <-
read.table("1998res_x.txt",header=TRUE)
dim(dat2)
m1 <- as.matrix(dat1)
m2 <- as.matrix(dat2)
vec1 <-
paste0(rownames(m1)[row(m1)],colnames(m1)[col(m1)])
vec2 <- paste0(rownames(m2)[row(m2)],colnames(m2)[col(m2)])
indx <- match(vec1,vec2)
indx1 <- indx[!is.na(indx)]
indx2 <- match(vec2,vec1)
indx2N <- indx2[!is.na(indx2)]
m1[indx2N] <- m2[indx1]
Thanks a lot!!
Best,
Elio
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