Read all files in a folder and apply a function to each data frame

Question

I am doing a relatively simple piece of analysis that I have put into a function on all the files in a particular folder. I was wondering whether anyone had any tips to help me automate the process on a number of different folders.

1. Firstly, I was wondering whether there was a way of reading all the files in a particular folder straight into R. I believe the following command will list all the files:

files <- (Sys.glob("*.csv"))

...which I found from Using R to list all files with a specified extension

And then the following code reads all those files into R.

listOfFiles <- lapply(files, function(x) read.table(x, header = FALSE))  

…from Manipulating multiple files in R

But the files seem to be read in as one continuous list and not individual files… how can I change the script to open all the csv files in a particular folder as individual dataframes?

2. Secondly, assuming that I can read all the files in separately, how do I complete a function on all these dataframes in one go. For example, I have created four small dataframes so I can illustrate what I want:

    Df.1 <- data.frame(A = c(5,4,7,6,8,4),B = (c(1,5,2,4,9,1)))  Df.2 <- data.frame(A = c(1:6),B = (c(2,3,4,5,1,1)))  Df.3 <- data.frame(A = c(4,6,8,0,1,11),B = (c(7,6,5,9,1,15)))  Df.4 <- data.frame(A = c(4,2,6,8,1,0),B = (c(3,1,9,11,2,16))) 

I have also made up an example function:

Summary<-function(dfile){ SumA<-sum(dfile$A) MinA<-min(dfile$A) MeanA<-mean(dfile$A) MedianA<-median(dfile$A) MaxA<-max(dfile$A)  sumB<-sum(dfile$B) MinB<-min(dfile$B) MeanB<-mean(dfile$B) MedianB<-median(dfile$B) MaxB<-max(dfile$B)  Sum<-c(sumA,sumB) Min<-c(MinA,MinB) Mean<-c(MeanA,MeanB) Median<-c(MedianA,MedianB) Max<-c(MaxA,MaxB) rm(sumA,sumB,MinA,MinB,MeanA,MeanB,MedianA,MedianB,MaxA,MaxB)  Label<-c("A","B") dfile_summary<-data.frame(Label,Sum,Min,Mean,Median,Max) return(dfile_summary)} 

I would ordinarily use the following command to apply the function to each individual dataframe.

Df1.summary<-Summary(dfile)

Is there a way instead of applying the function to all the dataframes, and use the titles of the dataframes in the summary tables (i.e. Df1.summary).

Many thanks,

Katie

Answer 1

On the contrary, I do think working with list makes it easy to automate such things.

Here is one solution (I stored your four dataframes in folder temp/).

filenames <- list.files("temp", pattern="*.csv", full.names=TRUE) ldf <- lapply(filenames, read.csv) res <- lapply(ldf, summary) names(res) <- substr(filenames, 6, 30) 

It is important to store the full path for your files (as I did with full.names), otherwise you have to paste the working directory, e.g.

filenames <- list.files("temp", pattern="*.csv") paste("temp", filenames, sep="/") 

will work too. Note that I used substr to extract file names while discarding full path.

You can access your summary tables as follows:

> res$`df4.csv`        A              B          Min.   :0.00   Min.   : 1.00    1st Qu.:1.25   1st Qu.: 2.25    Median :3.00   Median : 6.00    Mean   :3.50   Mean   : 7.00    3rd Qu.:5.50   3rd Qu.:10.50    Max.   :8.00   Max.   :16.00   

If you really want to get individual summary tables, you can extract them afterwards. E.g.,

for (i in 1:length(res))   assign(paste(paste("df", i, sep=""), "summary", sep="."), res[[i]])