Counting the number of rows of a series of csv files
Solution 1
read.csv
expects to read just one file, so you need to loop over files, a R idiomatic way of doing so is to use sapply
:
nrows <- sapply( csvfile, function(f) nrow(read.csv(f)) )
sum(nrows)
For example, here is a rewrite of your complete
function:
complete <- function(directory,id = 1:332) {
csvfiles <- sprintf("/Users/gcameron/Desktop/%s/%03d.csv", directory, id)
nrows <- sapply( csvfiles, function(f) nrow(read.csv(f)) )
sum(nrows)
}
Solution 2
Homework problems usually get tagged as such, though I don't know if that is required, but this clearly is homework.
Your function as written expects that id is not a vector (despite the default value being a vector of integers).
Change it to either use one of the *apply functions (more concise and common), or even an explicit loop. For each element in the id vector, you must call a function that opens that file and counts the observations.
This stackoverflow post has a good explanation of the differences between the *apply functions.
Doug Fir
Updated on July 09, 2022Comments
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Doug Fir almost 2 years
I'm working through an R tutorial and suspect that I have to use one of these functions but I'm not sure which (Yes I researched them but until I become more fluent in R terminology they are quite confusing).
In my working directory there is a folder "specdata". Specdata contains hundreds of CSV files named 001.csv - 300.csv.
The function I am working on must count the total number of rows for an inputed number of csv files. So if the argument in the function is
1:10
and each of those files has ten rows, return 100.Here's what I have so far:
complete <- function(directory,id = 1:332) { setpath <- paste("/Users/gcameron/Desktop",directory,sep="/") setwd(setpath) csvfile <- sprintf("%03d.csv", id) file <- read.csv(csvfile) nrow(file) }
This works when the ID argument is one number, say 17. But, if I input say 10:50 as an argument, I receive an error:
Error in file(file, "rt") : invalid 'description' argument
What should I do to be able to count the total number of rows from the inputed ID parameter?
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plannapus over 11 years
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Doug Fir over 11 yearsThanks. So few follow up Q's if you have a sec. 1) Where do I put this line? Within the function "complete" or after it? 2) If after it, do I not have to declare the object csvfile again for scope? 3) Your parameter "function(f)" - is that just the name of the function I made in it's place? i.e. nrows <- sapply( csvfile, complete(f# what goes here?) nrow(read.csv(f) As you can no doubt tell I'm struggling a bit with this
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Romain Francois over 11 yearsI've edited my answer. also note that your original function never reset the working directory when it is done, that's wrong.
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Tim B over 11 yearsok, thanks. I looked to see if that was covered in the faq, but didn't see it. I still think it's useful to know when it is homework, as I'm willing to provide a complete answer for someone trying to finish something at work, but would rather give hints and direction for homework.
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Doug Fir over 11 yearsThanks a ton I'm really grateful for this. That has worked. Having now seen it I can make sense of it.
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plannapus over 11 yearsThis is indeed a good point, and I thought too that they would have added that to the faq since most users don't read the blog or metaSE.
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Richie Cotton over 11 years
length(count.fields(f))
is probably a lot quicker thannrow(read.csv(f))
. (You can test this hypothesis withsystem.time
.) -
Dan Ciborowski - MSFT over 10 yearsI get a "Error in cc$id : $ operator is invalid for atomic vectors" error from trying this method.