Question

I have a simple function in R that runs summary() via lapply() on many CSVs from one directory that I specify. The function is shown below:

#   id -- the file name (i.e. 001.csv) so ID == 001. 
#   directory -- location of the CSV files (not my working directory)
#   summarize -- boolean val if summary of the CSV to be output to console. 
getMonitor <- function(id, dir, summarize = FALSE) 
{
    fl <- list.files(dir, pattern = "*.csv", full.names = FALSE)

    fdl <- lapply(fl, read.csv)

    dataSummary <- lapply(fdl, summary)

    if(summarize == TRUE)
    { dataSummary[[id]] }
}

When I try to specify the directory and then pass it as a parameter to the function like so:

dir <- "C:\\Users\\ST\\My Documents\\R\\specdata"
funcVar <-  getMonitor("001", dir, FALSE)

I receive the error:

Error in file(file, “rt”) : cannot open the connection. In addition: Warning message:
In file(file, “rt”) : cannot open file ‘001.csv’: No such file or directory

Yet when I run the code below on its own:

fl <- list.files("C:\\Users\\ST\\My Documents\\R\\specdata", 
                  pattern = "*.csv", 
                  full.names = FALSE)
fl[1]

It find the directory I’m pointing to and fl[1] correctly outputs [1] “001.csv” which is the first file listed.

My question is what am I doing wrong when trying to pass this path variable as a parameter to my function. Is R incapable of handling a parameter this way? Is there something I’m just completely missing? I’ve tried searching around and am familiar with other programming languages so, frankly, I feel kind of stupid/defeated for getting stuck on this right now.

Answer 1

You’re passing fl[1] directly to read.csv with the qualifying path. If, instead, you use full.names=TRUE you’ll get the full path and your read.csv step will work properly. However, you’ll have to do a little munge to make your if statement function again.

You could also expand on your lapply function to paste the directory and file name together:

fdl <- lapply(fl, function(x) read.csv(paste(dir, x, sep='\\')))

Or create this pasted full path in a separate line:

fl.qualified <- paste(dir, fl, sep='\\')
fdl <- lapply(fl.qualified, read.csv)

When you do the paste step, if you want to be really explicit, I would encourage a regex to make sure you don’t have someone passing a directory with a trailing slash:

fl.qualified <- paste(gsub('\\\\$', '', dir), f1, sep='\')

or something along those lines.