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Soheila Khodakarim

2012-Feb-17 11:44 UTC

[R] (subscript) logical subscript too long in using apply

Dear ALL
I have this function in R:



func_LN <- function(data){

med_ge <- matrix(c(rep(NA,nrow(data)*ncol(data))), nrow = nrow(data),
ncol=ncol(data), byrow=TRUE)
T <- matrix(c(rep(NA,length(n)*ncol(data))), nrow = length(n),
ncol=ncol(data), byrow=TRUE)
Tdiff<- matrix(c(rep(NA,length(n)*ncol(data))), nrow = length(n),
ncol=ncol(data), byrow=TRUE)
T1<- c(rep(NA,ncol(data)))
T0<- c(rep(NA,ncol(data)))
cov_rank<-matrix(c(rep(NA,ncol(data)*ncol(data))), nrow = ncol(data), ncol
= ncol(data) , byrow=TRUE)

med <- c(rep(NA,ncol(data)))
mean_ge <- c(rep(NA,ncol(data)))
n<-c(NA,2)
  if (ncol(data)>1){
    for(m_j in 1:ncol(data)){
      med[m_j]<-median(data[,m_j])}


    for(m_j in 1:ncol(data))
      for(m_i in 1:nrow(data))
      {
        if(data[m_i,m_j]>med[m_j])
          med_ge[m_i,m_j]=0
        else
          med_ge[m_i,m_j]=1
      }

    y=c(1,1,1,1,1,1,0,0,0,0)


    n<-c(sum(y == 1),sum(y==0))
    touse3 <- y==1

    T1<- apply(med_ge[touse3,], 2, mean)
    T0<- apply(med_ge[!touse3,], 2, mean)


    T=rbind(T1,T0)
    Tbar=colMeans(T)
    Tdiff=T-Tbar
    cov_rank=cov(med_ge)
    inv_cov_rank=ginv(cov_rank)

    LN=0
    for(m_i in 1:length(n)) {
      LN <-  LN+((Tdiff[m_i,]%*%inv_cov_rank)%*%t(Tdiff)[,m_i])*n[m_i]

    }
    return(LN)
  }}

func_LN(data)

Now, I want to try this function on subgroups of data.
So I used "apply"
 result <- apply(gs , 1 , function(z) func_LN(data[which(z==1),]))

but I saw this error:

Error in apply(med_ge[touse3, ], 2, mean) :
  (subscript) logical subscript too long

I will appreciate if you help me.

PS:the elements of gs are 1 0r 0.
dim(data)=24*2665
dim(gs)=107*2665

Soheila

	[[alternative HTML version deleted]]

Petr Savicky

2012-Feb-17 12:10 UTC

head link

[R] (subscript) logical subscript too long in using apply

On Fri, Feb 17, 2012 at 12:44:44PM +0100, Soheila Khodakarim
wrote:> Dear ALL
> I have this function in R:
> 
> 
> 
> func_LN <- function(data){
> 
> med_ge <- matrix(c(rep(NA,nrow(data)*ncol(data))), nrow = nrow(data),
> ncol=ncol(data), byrow=TRUE)
> T <- matrix(c(rep(NA,length(n)*ncol(data))), nrow = length(n),
> ncol=ncol(data), byrow=TRUE)
> Tdiff<- matrix(c(rep(NA,length(n)*ncol(data))), nrow = length(n),
> ncol=ncol(data), byrow=TRUE)
> T1<- c(rep(NA,ncol(data)))
> T0<- c(rep(NA,ncol(data)))
> cov_rank<-matrix(c(rep(NA,ncol(data)*ncol(data))), nrow = ncol(data),
ncol
> = ncol(data) , byrow=TRUE)
> 
> med <- c(rep(NA,ncol(data)))
> mean_ge <- c(rep(NA,ncol(data)))
> n<-c(NA,2)
>   if (ncol(data)>1){
>     for(m_j in 1:ncol(data)){
>       med[m_j]<-median(data[,m_j])}
> 
> 
>     for(m_j in 1:ncol(data))
>       for(m_i in 1:nrow(data))
>       {
>         if(data[m_i,m_j]>med[m_j])
>           med_ge[m_i,m_j]=0
>         else
>           med_ge[m_i,m_j]=1
>       }
> 
>     y=c(1,1,1,1,1,1,0,0,0,0)
> 
> 
>     n<-c(sum(y == 1),sum(y==0))
>     touse3 <- y==1
> 
>     T1<- apply(med_ge[touse3,], 2, mean)
>     T0<- apply(med_ge[!touse3,], 2, mean)
> 
> 
>     T=rbind(T1,T0)
>     Tbar=colMeans(T)
>     Tdiff=T-Tbar
>     cov_rank=cov(med_ge)
>     inv_cov_rank=ginv(cov_rank)
> 
>     LN=0
>     for(m_i in 1:length(n)) {
>       LN <-  LN+((Tdiff[m_i,]%*%inv_cov_rank)%*%t(Tdiff)[,m_i])*n[m_i]
> 
>     }
>     return(LN)
>   }}
> 
> func_LN(data)
> 
> Now, I want to try this function on subgroups of data.
> So I used "apply"
>  result <- apply(gs , 1 , function(z) func_LN(data[which(z==1),]))
> 
> but I saw this error:
> 
> Error in apply(med_ge[touse3, ], 2, mean) :
>   (subscript) logical subscript too long
> 
> I will appreciate if you help me.
> 
> PS:the elements of gs are 1 0r 0.
> dim(data)=24*2665
> dim(gs)=107*2665
Hi.

Without a reproducible example, it is hard to determine
the problem. You can try  options(error=utils::recover)
to get more information on the values of the variables
when the error occurs.

However, i am not sure, why you use data[which(z==1),]
and not data[,which(z==1)]. The reason is that the
function "apply(gs , 1 , func)" applies "func" to the
rows of "gs". These rows have length 2665, which is equal
to the number of columns of "data". So, i would expect
to use "z" to select columns, not rows of "data". Can you
comment on this?

Petr Savicky.

Petr PIKAL

2012-Feb-17 12:24 UTC

head link

[R] (subscript) logical subscript too long in using apply

Hi

apply probably does not understand you function. I do not want to go too 
deeply into it but I noticed few issues in it. See inline
> 
> Dear ALL
> I have this function in R:
> 
> 
> 
> func_LN <- function(data){
> 
> med_ge <- matrix(c(rep(NA,nrow(data)*ncol(data))), nrow = nrow(data),
> ncol=ncol(data), byrow=TRUE)
> T <- matrix(c(rep(NA,length(n)*ncol(data))), nrow = length(n),
> ncol=ncol(data), byrow=TRUE)
> Tdiff<- matrix(c(rep(NA,length(n)*ncol(data))), nrow = length(n),
> ncol=ncol(data), byrow=TRUE)
> T1<- c(rep(NA,ncol(data)))
> T0<- c(rep(NA,ncol(data)))
> cov_rank<-matrix(c(rep(NA,ncol(data)*ncol(data))), nrow = ncol(data), 
ncol> = ncol(data) , byrow=TRUE)
> 
> med <- c(rep(NA,ncol(data)))
> mean_ge <- c(rep(NA,ncol(data)))
> n<-c(NA,2)
>   if (ncol(data)>1){
>     for(m_j in 1:ncol(data)){
>       med[m_j]<-median(data[,m_j])}
this shall be the same as
med <- apply(data, 2, median)

> 
> 
>     for(m_j in 1:ncol(data))
>       for(m_i in 1:nrow(data))
>       {
>         if(data[m_i,m_j]>med[m_j])
>           med_ge[m_i,m_j]=0
>         else
>           med_ge[m_i,m_j]=1
>       }
AFAIK this shall be same as

med_ge<-(sweep(dat, 2, med)<=0)*1
> 
>     y=c(1,1,1,1,1,1,0,0,0,0)
> 
> 
>     n<-c(sum(y == 1),sum(y==0))
>     touse3 <- y==1
> 
>     T1<- apply(med_ge[touse3,], 2, mean)
>     T0<- apply(med_ge[!touse3,], 2, mean)
> 
> 
>     T=rbind(T1,T0)
>     Tbar=colMeans(T)
>     Tdiff=T-Tbar
>     cov_rank=cov(med_ge)
>     inv_cov_rank=ginv(cov_rank)
> 
>     LN=0
>     for(m_i in 1:length(n)) {
>       LN <-  LN+((Tdiff[m_i,]%*%inv_cov_rank)%*%t(Tdiff)[,m_i])*n[m_i]
> 
>     }
>     return(LN)
>   }}
> 
> func_LN(data)
> 
> Now, I want to try this function on subgroups of data.
> So I used "apply"
>  result <- apply(gs , 1 , function(z) func_LN(data[which(z==1),]))
> 
> but I saw this error:
> 
> Error in apply(med_ge[touse3, ], 2, mean) :
>   (subscript) logical subscript too long
The rest is quite complicated for me so I do not dig into it. The obvious 
source of error is 
apply(med_ge[touse3, ], 2, mean)

which tells you that touse3 is longer than number of med_ge rows.

The error message probably could not be more precise.

Regards
Petr



> 
> I will appreciate if you help me.
> 
> PS:the elements of gs are 1 0r 0.
> dim(data)=24*2665
> dim(gs)=107*2665
> 
> Soheila
> 
>    [[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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