Shery Shery - 2 months ago 66x
R Question

Reading multiple files and calculating mean based on user input

I am trying to write a function in R which takes 3 inputs:

  1. Directory

  2. pollutant

  3. id

I have a directory on my computer full of CSV's files i.e. over 300. What this function would do is shown in the below prototype:

pollutantmean <- function(directory, pollutant, id = 1:332) {
## 'directory' is a character vector of length 1 indicating
## the location of the CSV files

## 'pollutant' is a character vector of length 1 indicating
## the name of the pollutant for which we will calculate the
## mean; either "sulfate" or "nitrate".

## 'id' is an integer vector indicating the monitor ID numbers
## to be used

## Return the mean of the pollutant across all monitors list
## in the 'id' vector (ignoring NA values)

An example output of this function is shown here:

pollutantmean("specdata", "sulfate", 1:10)

## [1] 4.064

pollutantmean("specdata", "nitrate", 70:72)

## [1] 1.706

pollutantmean("specdata", "nitrate", 23)

## [1] 1.281

I can read the whole thing in one go by:

path = "C:/Users/Sean/Documents/R Projects/Data/specdata"
fileList = list.files(path=path,pattern="\\.csv$",full.names=T) = lapply(fileList,read.csv,header=TRUE)
DATA ="rbind",

My issue are:

  1. User enters id either atomic or in a range e.g. suppose user enters 1 but the file name is 001.csv or what if user enters a range 1:10 then file names are 001.csv ... 010.csv

  2. Column is enetered by user i.e. "sulfate" or "nitrate" which he/she is interested in getting the mean of...There are alot of missing values in these columns (which i need to omit from the column before calculating the mean.

The whole data from all the files look like this :

Date sulfate nitrate ID
2004-01-01: 250 Min. : 0.0 Min. : 0.0 Min. : 1.0
2004-01-02: 250 1st Qu.: 1.3 1st Qu.: 0.4 1st Qu.: 79.0
2004-01-03: 250 Median : 2.4 Median : 0.8 Median :168.0
2004-01-04: 250 Mean : 3.2 Mean : 1.7 Mean :164.5
2004-01-05: 250 3rd Qu.: 4.0 3rd Qu.: 2.0 3rd Qu.:247.0
2004-01-06: 250 Max. :35.9 Max. :53.9 Max. :332.0
(Other) :770587 NA's :653304 NA's :657738

Any idea how to formulate this would be highly appreciated...



That's the way I fixed it:

pollutantmean <- function(directory, pollutant, id = 1:332) {
    #set the path
    path = directory

    #get the file List in that directory
    fileList = list.files(path)

    #extract the file names and store as numeric for comparison
    file.names = as.numeric(sub("\\.csv$","",fileList))

    #select files to be imported based on the user input or default
    selected.files = fileList[match(id,file.names)]

    #import data
    Data = lapply(file.path(path,selected.files),read.csv)

    #convert into data frame
    Data =,Data)

    #calculate mean


The last question is that my function should call "specdata" (the directory name where all the csv's are located) as the directory, is there a directory type object in r?

suppose i call the function as:

pollutantmean(specdata, "niterate", 1:10)

It should get the path of specdata directory which is on my working directory... how can I do that?