Question

I have another question for the brilliant minds out there (this site is so addictive).

I am running some simulations on a matrix and I have nested for loops for this purpose. The first creates a vector that increases by one each time a loop cycles. The nested loop is running simulations by randomizing the vector, attaching it to the matrix, and calculating some simple properties on the new matrix. (For an example, I used properties that will not vary in the simulations, but in practice I require the simulations to get a good idea of the impact of the randomized vector.) The nested loop runs 100 simulations, and ultimately I want only the column means of those simulations.

Here’s some example code:

property<-function(mat){                       #where mat is a matrix
  a=sum(mat) 
  b=sum(colMeans(mat))
  c=mean(mat)
  d=sum(rowMeans(mat))
  e=nrow(mat)*ncol(mat)
  answer=list(a,b,c,d,e)
  return(answer)
  }

x=matrix(c(1,0,1,0, 0,1,1,0, 0,0,0,1, 1,0,0,0, 1,0,0,1), byrow=T, nrow=5, ncol=4)

obj=matrix(nrow=100,ncol=5,byrow=T)            #create an empty matrix to dump results into

for(i in 1:ncol(x)){                           #nested for loops
  a=rep(1,times=i)                             #repeat 1 for 1:# columns in x
  b=rep(0,times=(ncol(x)-length(a)))           #have the rest of the vector be 0
  I.vec=append(a,b)                            #append these two for the I vector
    for (j in 1:100){
      I.vec2=sample(I.vec,replace=FALSE)       #randomize I vector
      temp=rbind(x,I.vec2)
      prop<-property(temp)
      obj[[j]]<-prop
      }
  write.table(colMeans(obj), 'myfile.csv', quote = FALSE, sep = ',', row.names = FALSE)
  }

The problem I am encountering is how to fill in the empty object matrix with the results of the nested loop. obj ends up as a vector of mostly NAs, so it is clear that I am not assigning the results properly. I want each cycle to add a row of prop to obj, but if I try

obj[j,]<-prop

R tells me that there is an incorrect number of subscripts on the matrix.

Thank you so much for your help!

EDITS:
Okay, so here is the improved code re the answers below:

property<-function(mat){                       #where mat is a matrix
  a=sum(mat)
  b=sum(colMeans(mat))
  f=mean(mat)
  d=sum(rowMeans(mat))
  e=nrow(mat)*ncol(mat)
  answer=c(a,b,f,d,e)
  return(answer)
  }

x=matrix(c(1,0,1,0, 0,1,1,0, 0,0,0,1, 1,0,0,0, 1,0,0,1), byrow=T, nrow=5, ncol=4)

obj<-data.frame(a=0,b=0,f=0,d=0,e=0)            #create an empty dataframe to dump results into
obj2<-data.frame(a=0,b=0,f=0,d=0,e=0)

for(i in 1:ncol(x)){                           #nested for loops
  a=rep(1,times=i)                             #repeat 1 for 1:# columns in x
  b=rep(0,times=(ncol(x)-length(a)))           #have the rest of the vector be 0
  I.vec=append(a,b)                            #append these two for the I vector
    for (j in 1:100){
      I.vec2=sample(I.vec,replace=FALSE)       #randomize I vector
      temp=rbind(x,I.vec2)
      obj[j,]<-property(temp)
      }
  obj2[i,]<-colMeans(obj)
  write.table(obj2, 'myfile.csv', quote = FALSE,
  sep = ',', row.names = FALSE, col.names=F, append=T)
  }

However, this is still glitchy, as the myfile should only have four rows (one for each column of x), but actually has 10 rows, with some repeated. Any ideas?

Answer 1

Your property function is returning a list. If you want to store the numbers in a matrix, you should have it return a numeric vector:

property <- function(mat)
{
  ....
  c(a, b, c, d, e)  # probably a good idea to rename your "c" variable
}

Alternatively, instead of defining obj to be a matrix, make it a data.frame (which conceptually makes more sense, as each column represents a different quantity).

obj <- data.frame(a=0, b=0, c=0, ...)
for(i in 1:ncol(x))
  ....
  obj[j, ] <- property(temp)

Finally, note that your call to write.table will overwrite the contents of myfile.csv, so the only output it will contain is the result for the last iteration of i.