Question

I am writing a loop that takes two files per run e.g.a0.txt and b0.txt. I am running this over 100 files that run from a0.txt and b0.txt to a999.txt and b999.txt. The pattern function i use works perfect if i do the run for files a0 and b0 to a9 and b9 with only file pairs 0-9 in the directory. but when i put more files in the directory and do the run from ‘0:10, the loop fails and confuses vectors in files. I think this is becuase of thepattern` i use i.e.

 list.files(pattern=paste('.', x, '\\.txt', sep=''))

This only looks for files that have '.',x,//txt.

So if '.'=a and x=1 it finds file a1. But i think it gets confused between a0 and a10 when I do the run over more files. But i cannot seem to find the appropriate loop that will serach for files that also look for files up to a999 and b999, as well.

Can anyone help with a better way to do this? code below.

dostuff <- function(x) 
{
files <- list.files(pattern=paste('.', x, '\\.txt', sep=''))
a <- read.table(files[1],header=FALSE)  #file a0.txt 
G <- a$V1-a$V2
b <- read.table(files[2],header=FALSE) #file b0.txt
as.factor(b$V2)
q <- tapply(b$V3,b$V2,Fun=length)
H <- b$V1-b$V2
model <- lm(G~H)
return(model$coefficients[2],q)
}

results <- sapply(0:10,dostuff)
Error in tapply(b$V3, b$V2, FUN = length) : arguments must have same length

Answer 1

How about getting the files directly, without searching. i.e.

dostuff <- function(x) 
{
    a.filename <- paste('a', x, '.txt', sep='') # a<x>.txt
    b.filename <- paste('b', x, '.txt', sep='') # b<x>.txt
    a <- read.table(a.filename, header=FALSE)  
    # [...]
    b <- read.table(b.filename, header=FALSE)
    # [...]
}

But the error message says the problem is caused by the call to tapply rather than anything about incorrect file names, and I have literally no idea how that could happen, since I thought a data frame (which read.table creates) always has the same number of rows for each column. Did you copy-paste that error message out of R? (I have a feeling there might be a typo, and so it was, for example, q <- tapply(a$V3,b$V2,Fun=length). But I could easily be wrong)

Also, as.factor(b$V2) doesn’t modify b$V2, it just returns a factor representing b$V2: after you call as.factor b$V2 is still a vector. You need to assign it to something, e.g.:

V2.factor <- as.factor(b$V2)