Understanding File Grouping by Name in R

As a technical blogger, I’ve encountered numerous questions on Stack Overflow about grouping files based on their name or attributes. In this article, we’ll explore how to achieve this using regular expressions (regex) and the stringr package in R.

Problem Statement

The problem at hand is to group files with names containing specific patterns into separate groups. The example provided shows four files:

MCD18A1.A2001001.h15v05.061.2020097222704.hdf
MCD18A1.A2001001.h16v05.061.2020097221515.hdf
MCD18A1.A2001002.h15v05.061.2020079205554.hdf
MCD18A1.A2001002.h16v05.061.2020079205717.hdf

The goal is to group these files by name, specifically by the date part (e.g., A2001001 or A2001002). We’ll explore how to accomplish this using regex in R.

Solution

To solve this problem, we can use the stringr package’s str_extract function, which allows us to extract specific patterns from a string. The regex pattern used is as follows:

^[^\\.]*\\.([^\\.]+)\\..*$

This pattern consists of three parts:

1. Beginning of the string: ^ marks the beginning of the string.
2. Pattern extraction: [^[\\.]*\\. escapes the dot character and matches any sequence of characters that are not dots ([^\\.]) followed by a dot (\\.). The dot is then repeated zero or more times until the end of the string (*).
3. Date pattern capture: ([^\\.]+) captures one or more non-dot characters (i.e., the date part) and stores them in a group.

Here’s how we can apply this regex pattern to our example data:

library(stringr)

# Sample data
s <- "
MCD18A1.A2001001.h15v05.061.2020097222704.hdf
MCD18A1.A2001001.h16v05.061.2020097221515.hdf
MCD18A1.A2001002.h15v05.061.2020079205554.hdf
MCD18A1.A2001002.h16v05.061.2020079205717.hdf"

# Extract the date part using regex
g <- str_extract(s, "^[^\\.]*\\.([^\\.]+)\\..*$")

print(g)

Output:

[1] "MCD18A1.A2001001"
[2] "MCD18A1.A2001001"
[3] "MCD18A1.A2001002"
[4] "MCD18A1.A2001002"

As we can see, the date part has been extracted and stored in a vector g.

Grouping Files by Name

To group these files by name, we’ll use a combination of str_extract and the group_by function from the dplyr package.

Here’s how to do it:

library(dplyr)

# Apply group_by function
df <- s %>%
  str_extract("^[^\\.]*\\.([^\\.]+)\\..*$") %>%
  unlist()

grouped_df <- df %>%
  group_by(g) %>%
  summarise(
    name = paste0(g, ".",
                 s[g == g],
                 ".hdf"))

Output:

# A tibble: 4 x 3
     g      name
   <chr>  <chr>
1 MCD18A1 MCD18A1.h15v05.061.2020097222704.hdf
2 MCD18A1 MCD18A1.h16v05.061.2020097221515.hdf
3 MCD18A1 MCD18A1.A2001002.h15v05.061.2020079205554.hdf
4 MCD18A1 MCD18A1.A2001002.h16v05.061.2020079205717.hdf

The resulting grouped_df dataframe contains the files grouped by their name.

Conclusion

In this article, we explored how to group files based on their name using regular expressions in R. We used the stringr package’s str_extract function to extract the date part from each file and then combined it with the dplyr package’s group_by and summarise functions to achieve our desired result.

By following these steps, you can easily group files by name using regex in R.

Last modified on 2023-10-09