Calculating Total Drug Duration Using R: A Step-by-Step Guide

In this article, we will discuss how to calculate the total duration of drug use for each patient in a given dataset. We will explore different approaches and provide examples using both base R and data.table packages.

Introduction

Calculating the total duration of drug use is an important aspect of pharmaceutical research and clinical trials. It allows researchers to assess the effectiveness of a medication over time and identify potential risks associated with long-term treatment. In this article, we will walk through the process of creating a variable for total drug duration using R.

Problem Statement

Given a dataset containing patient information, including their ID, dosage, start date, and stop date, we need to create a variable that represents the total duration of drug use for each patient.

# Sample dataset
data <- structure(
  list(
    Id = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
    time = 1:20,
    Event = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L),
    Fup = c(90L, 90L, 90L, 90L, 90L, 90L, 90L, 90L, 90L, 90L),
    Start = 1:20,
    Stop = 2:21,
    dose = c(0, 0, 2.6, 2.6, 2.6, 2.6, 2.6, 2.6, 2.6, 2.6)
  ),
  class = "data.frame"
)

# Get unique patient IDs
list.id <- unique(data$Id)
nbr.subjects <- length(list.id)

# Initialize total duration variable to NULL
tot.dur.use <- NULL

# Loop through each patient ID
for (i in 1:nbr.subjects) {
  # Filter data for current patient
  current.subject <- data[data$Id == list.id[i], ]
  
  # Calculate total dose duration (excluding 0 doses)
  tot.dur.use.tmp <- sum(current.subject$dose != 0)
  
  # Update total duration variable
  if (i == 1) {
    tot.dur.use <- c(tot.dur.use, tot.dur.use.tmp)
  } else {
    tot.dur.use <- c(tot.dur.use, tot.dur.use.tmp)
  }
}
data <- cbind(data, tot.dur.use)

# Error message: arguments imply differing number of rows

Data.table Solution

Using data.table Package

One way to solve this problem is by using the data.table package. Here’s how you can do it:

library("data.table")

setDT(data)

# Calculate total dose duration for each patient
data[, tot.dur := cumsum(dose), by=Id]

# Print updated dataset
data

Alternative Solution: Running Count

If you want a running count that excludes 0 doses, you can use the following code:

# Function to calculate running total (excluding 0)
length2 <- function(x) {
  x[x != 0] <- 1:length(x[x != 0])
  return(x[x != 0])
}

# Apply function to dataset
data[, lapply(.SD, length), by=Id]

Alternative Solution: Aggregate by Patient ID

To aggregate the total non-zero dose count for each patient, you can use the following code:

# Filter out rows with 0 doses
data2 <- data[dose != 0]

# Calculate total non-zero dose count for each patient
data[, lapply(.SD, length), by=Id]

Conclusion

In this article, we discussed how to create a variable for total drug duration using R. We explored different approaches and provided examples using both base R and data.table packages. By following the steps outlined in this article, you should be able to calculate the total duration of drug use for each patient in your dataset.

References

• ?data.table (data.table package documentation)
• ?cumsum (base R function documentation)

Last modified on 2023-08-07