Understanding the `eem_import_dir` Function in R: Workaround for Processing Multiple Files

Understanding the `eem_import_dir` Function in R

The eem_import_dir function from the staRdom package is designed to read and combine multiple files with a specific pattern. However, when this function is called, it seems that only one file is being read at a time, and not all combined as expected.

In R, file system navigation can be complex due to the nature of the operating system. The dir() function returns an object containing information about each file in the specified directory, including subdirectories. However, when working with file patterns, it is essential to understand how R’s pattern matching works.

Pattern Matching in R

R’s pattern matching uses regular expressions (regex) under the hood. When you specify a pattern while calling dir(), R looks for files or directories that match this pattern. The $ symbol in the pattern specifies that it should only match at the end of the string, and the . wildcard matches any single character.

In the case of the eem_import_dir() function, the pattern ".RData$|.RDa$", with ignore.case = TRUE, will find files with names ending in .RData or .RDa$. This ensures that R reads all files with these extensions, regardless of their case.

The `eem_files` Variable: A List of Matching Files

When the dir() function is called with a specified pattern, it returns an object containing information about each matching file. In this case, the returned object is stored in the variable eem_files. This list contains objects representing individual files or subdirectories.

Iterating Over the `eem_files` List

The next step in the eem_import_dir() function involves iterating over the eem_files list and performing specific actions on each file. However, it seems that only one file is being processed at a time. Let’s dive deeper into this section.

The Looping Mechanism of `eem_import_dir()`

The main loop in the eem_import_dir() function starts with:

for (file in eem_files) {
  file <- load(file)

This loop iterates over each object in the eem_files list, loading it into memory using the load() function. The variable file now holds a reference to this loaded object.

However, there is an issue here: after loading and storing the current file in the file variable, the NULL statement is executed immediately after:

NULL

This means that any further processing on the file within the loop is bypassed. It’s as if the loop only checks the eem_files list once, but doesn’t actually process each item individually.

Why Only One File Is Being Processed

The primary reason why only one file seems to be processed at a time is due to the nature of R’s list processing mechanism and the presence of the NULL statement. The loop iterates over the elements in eem_files, but when it encounters the first item, it executes the code inside the loop without passing control back to the loop.

To make things worse, any file that is loaded into memory using load(file) will be closed when it goes out of scope, which happens immediately after executing this line. This means that even though we’re iterating over multiple files in theory, each one’s lifetime is short-lived due to being immediately discarded when the code exits.

Workarounds

While this behavior might seem counterintuitive at first glance, there is a workaround for it: using tryCatch() instead of NULL inside your loop:

for (file in eem_files) {
  tryCatch(
    expr = {
      file <- load(file)
      if (get(file) %&gt;% class() == "eemlist") {
        if (exists("eem_list")) 
          eem_list <- eem_bind(eem_list, get(file))
        else eem_list <- get(file)
      }
    },
    error = function(e) {
      warning(paste0("Error processing file", file, ": ", e$message))
    }
  )
}

In this revised version of the loop, if an exception occurs while trying to process a file (like when get(file) fails), it gets caught by the outer tryCatch() block and printed as a warning. This way, each file is indeed processed individually.

Example Use Case

Here’s how you might use eem_import_dir() in your own R script:

# Load necessary libraries and set up working directory
library(staRdom)
setwd("path/to/your/eem/files")

# Call eem_import_dir()
files <- eem_import_dir()

# Now 'files' contains the combined eemlist object
print(files %&gt;% class()) # Should print: "eemlist"

In this example, we set up a working directory and call eem_import_dir() to combine all .RData or .RDa$ files in that directory into one.

Last modified on 2024-07-03