coursera air pollution assignment - r

Question

Using Mac OS 10.10.3
RStudio Version 0.98.1103
My working directory is a list of 332 .csv files and I set it correctly. Here's the code:
pollutantmean <- function(directory, pollutant, id = 1:332) {
all_files <- list.files(directory, full.names = T)
dat <- data.frame()
for(i in id) {
dat <- rbind(dat, read.csv(all_files[i]))
}
ds <- (dat[, pollutant], na.rm = TRUE)
mean(ds[, pollutant])
}
Part of the assignment is to get the mean of the first 10 numeric values of a pollutant. To do this, I used the call function (where "spectata" is the directory with 332 .csv files):
pollutantmean(specdata, "Nitrate", 1:10)
The error messages I get are:
**Error in file(file, "rt") : cannot open the connection
** In addition: Warning message: In file(file, "rt") : cannot open file 'NA': No such file or directory
Like many students that have posed questions here, I’m new to programming and to R and still distant from getting any results when calling my function. There are many questions and answers about this coursera assignment in stack overflow but my review of these exchanges hasn't addressed the bug in my code.
Anyone have a suggestion how to fix the bug?

Answer 1

In addition to the other answers is you can try this:
all_files <- list.files(directory, pattern="*.csv", full.names = TRUE)
to avoid select any other kind of file.
or even this strange one
all_files <- paste(directory, "\\", sprintf("%03d", id), ".csv", sep="")

Answer 2

I take the time to answer since the question comes back at every Coursera session.
First, be careful with the typo : Do call pollutantmean("specdata", "Nitrate", 1:10)
instead of pollutantmean(specdata, "Nitrate", 1:10.
Then your working directory should be the parent directory of "specdata" (for exemple, if your path was /dev/specdata, your working directory should have been /dev).
You can get the current working directory with getwd() and set the new one with setwd() (careful there, the path would be relative to the current working directory).

Answer 3

Add a line after all_files <- list.files(directory, full.names = TRUE) (it's a bad habit to use T instead of TRUE):
print(all_files)
Then call your function again, so you will see the content of that object. Then, check where are you working with getwd().

Answer 4

Modify your line no. 5 to dat <- rbind(dat, read.csv(i, comment.char = ""))
This will bind the data of all csv files to 'dat' dataframe.

Answer 5

Based upon the information provided, it can be assumed there are not 332 files in the directory you specify (if one attempts to access an index of a vector that is out of bounds, an NA is returned - hence the error "cannot open file 'NA'"). This is suggestive that the path you are using (which is not provided) points to a directory which does not contain the csv files (presuming there truly are 332 files in that directory). Some suggestions:
Check that the directory you are providing is accurate. Simply do a list.files to see what files exist in the directory you are using.
Use the pattern argument of list.files to be sure you are only going to read the csv files
Loop over the files using the length of the vector returned from list.files, rather than having to code this manually
You can add a sanity check to be sure you are reading all files by printing out each file, or returning a list containing the results and file names