Reduce unnecessary repeated reading from files in nested for loop R - r

Question

I'm writing some R code to handle pairs of files, an Excel and a csv (Imotions.txt). I need extract a column from the Excel and merge it to the csv, in pairs. Below is my abbreviated script: My script is now in polynomial time, and keeps repeating the body of the nested for loop 4 times instead of just doing it once.
Basically is there a general way to think about running some code over a paired set of files that I can translate to this and other languages?
excel_files <- list.files(pattern = ".xlsx" , full.names = TRUE)
imotion_files <-list.files(pattern = 'Imotions.txt', full.names = TRUE)
for (imotion_file in imotion_files) {
for (excel_file in excel_files) {
filename <- paste(sub("_Imotions.txt", "", imotion_file))
raw_data <- extract_raw_data(imotion_file)
event_data <- extract_event_data(imotion_file)
#convert times to milliseconds
latency_ms <- as.data.frame(
sapply(
df_col_only_ones$latency,
convert_to_ms,
raw_data_first_timestamp = raw_data_first_timestamp
)
)
#read in paradigm data
paradigm_data <- read_excel(path = excel_file, range = "H30:H328")
merged <- bind_cols(latency_ms, paradigm_data)
print(paste("writing = ", filename))
write.table(
merged,
file = paste(filename, "_EVENT", ".txt", sep = ""),
sep = '\t',
col.names = TRUE,
row.names = FALSE,
quote = FALSE
)
}
}

Answer 1

It is not entirely clear about some operations. Here is a an option in tidyverse
library(dplyr)
library(tidyr)
library(purrr)
library(stringr)
out <- crossing(excel_files, imotion_files) %>%
mutate(filename = str_remove(imotion_file, "_Imotions.txt"),
raw_data = map(imotion_files, extract_raw_data),
event_data = map(imption_filess, extract_event_data),
paradigm_data = map(excel_files, ~
read_excel(.x, range = "H30:H328") %>%
bind_cols(latency_ms, .))
Based on the OP's code, latency_ms can be created outside the loop once and used it while binding the columns

Answer 2

Based on the naming of raw_data_first_timestamp, I'm assuming it's created by the extract_raw_data function - otherwise you can move the latency_ms outside the loop entirely, as akrun mentioned.
If you don't want to use tidyverse, see the modified version of your code at bottom. Notice that the loops have been broken out to cut down on duplicated actions.
Some general tips to improve efficiency when working with loops:
Before attempting to improve nested loop efficiencies, consider whether the loops can be broken out so that data from earlier loops is stored for usage in later loops. This can also be done with nested loops and variables tracking whether data has already been set, but it's usually simpler to break the loops out and negate the need for the tracking variables.
Create variables and call functions before the loop where possible. Depending on the language and/or compiler (if one is used), variable creation outside loops may not help with efficiency, but it's still good practice.
Variables and functions which must be created or called inside loops should be done in the highest scope - or the outermost loop - possible.
Disclaimer - I have never used R, so there may be syntax errors.
excel_files <- list.files(pattern = ".xlsx" , full.names = TRUE)
imotion_files <-list.files(pattern = 'Imotions.txt', full.names = TRUE)
paradigm_data_list <- vector("list", length(excel_files))
for (i in 1:length(excel_files)) {
#read in paradigm data
paradigm_data_list[[i]] <- read_excel(path = excel_files[[i]], range = "H30:H328")
}
for (imotion_file in imotion_files) {
filename <- paste(sub("_Imotions.txt", "", imotion_file))
raw_data <- extract_raw_data(imotion_file)
event_data <- extract_event_data(imotion_file)
#convert times to milliseconds
latency_ms <- as.data.frame(
sapply(
df_col_only_ones$latency,
convert_to_ms,
raw_data_first_timestamp = raw_data_first_timestamp
)
)
for (paradigm_data in paradigm_data_list) {
merged <- bind_cols(latency_ms, paradigm_data)
print(paste("writing = ", filename))
write.table(
merged,
file = paste(filename, "_EVENT", ".txt", sep = ""),
sep = '\t',
col.names = TRUE,
row.names = FALSE,
quote = FALSE
)
}
}