Module 2: Data Wrangling and Visualization in Julia (Exercises)

Author

Jessica Wojciechowski

1 Module Introduction and Objectives

The target audience are pharmacometricians with experience in the R programming and statistical language and familiar with dataset preparation and exploratory data analysis in pharmacometrics. The Module makes reference to similarities and differences to R and builds on the concepts described in Module 1: Introduction to Julia.

The concepts and Julia packages showcased in this Module are:

All output DataFrames have been converted for presentation purposes using SummaryTables.jl.

1.1 Objectives

The objectives of the Module 2 exercises are to:

  1. Perform an exploratory data analysis on an example dataset and re-create the figures and tables presented using Julia
  2. Bonus Challenge: translate your existing analysis code for exploratory data analysis and data summaries from R (or current programming language) to Julia

The exercises are designed to be challenging and require reference to the Module materials and package documentation.

2 Exercise Setup

To obtain the example analysis dataset for all exercises, the PharmaDatasets package needs to be loaded. This is not the only package required to complete the exercises and you will need to load any additional packages.

# Load the PharmaDatasets package
using PharmaDatasets

The example analysis dataset can be obtained by:

# Load the warfarin dataset
warfarin_df = dataset("paganz2024/warfarin_long")

3 Summary Table of Demographics

Generate a summary table of the analysis population that appears as below:

Characteristic Total (n = 31)
Age (years)
Mean (SD) 30.4 (10.1)
Median (Min, Max) 27.0 (21.0, 63.0)
Missing (%) 0 (0.00)
Body Weight (kg)
Mean (SD) 70.1 (12.9)
Median (Min, Max) 73.3 (40.0, 102.)
Missing (%) 0 (0.00)
Sex; n (%)
Female 5 (16.1)
Male 26 (83.9)
Missing 0 (0.00)
Note

The aesthetics of the example table is only for presentation purposes only.

4 Summary of Observations Over Time

Create a numerical summary (mean and 90% confidence interval) of pharmacokinetic [PK] (DVID = 1) and pharmacodynamic [PD] (DVID = 2) observations over time, stratified by sex:

42×8 DataFrame
17 rows omitted
Row SEX DVID TIME nid mean_val sd_val lo90_val hi90_val
Cat… String Float64 Int64 Float64 Float64 Float64 Float64
1 Female Warfarin Concentration (mg/L) 0.5 2 0.0 0.0 0.0 0.0
2 Female Warfarin Concentration (mg/L) 1.0 3 3.43333 2.87112 -0.467701 7.33437
3 Female Warfarin Concentration (mg/L) 2.0 2 8.1 4.94975 -2.11995 18.3199
4 Female Warfarin Concentration (mg/L) 3.0 5 11.45 1.87697 9.75856 13.1414
5 Female Warfarin Concentration (mg/L) 6.0 5 11.9167 0.538207 11.4317 12.4017
6 Female Warfarin Concentration (mg/L) 9.0 5 11.45 1.41527 10.1746 12.7254
7 Female Warfarin Concentration (mg/L) 12.0 3 10.55 1.18181 8.94426 12.1557
8 Female Warfarin Concentration (mg/L) 24.0 5 7.66 1.29923 6.48919 8.83081
9 Female Warfarin Concentration (mg/L) 36.0 5 6.38 1.97028 4.60447 8.15553
10 Female Warfarin Concentration (mg/L) 48.0 5 4.7 1.9975 2.89994 6.50006
11 Female Warfarin Concentration (mg/L) 72.0 5 3.46 1.53721 2.07474 4.84526
12 Female Warfarin Concentration (mg/L) 96.0 5 1.98 1.11669 0.973686 2.98631
13 Female Warfarin Concentration (mg/L) 120.0 5 1.8 0.6245 1.23723 2.36277
31 Male Warfarin Concentration (mg/L) 48.0 26 6.26538 1.1541 5.87934 6.65143
32 Male Warfarin Concentration (mg/L) 72.0 26 4.4 0.848057 4.11633 4.68367
33 Male Warfarin Concentration (mg/L) 96.0 26 3.06923 0.761981 2.81435 3.32411
34 Male Warfarin Concentration (mg/L) 120.0 26 2.19615 0.619342 1.98898 2.40332
35 Male Prothrombin Complex Activity 0.0 26 97.1154 5.42827 95.2996 98.9311
36 Male Prothrombin Complex Activity 24.0 26 37.5385 5.74965 35.6152 39.4617
37 Male Prothrombin Complex Activity 36.0 26 24.3077 4.1547 22.9179 25.6974
38 Male Prothrombin Complex Activity 48.0 26 18.8077 4.10871 17.4333 20.1821
39 Male Prothrombin Complex Activity 72.0 26 20.0 6.08961 17.963 22.037
40 Male Prothrombin Complex Activity 96.0 26 24.16 8.89138 21.1858 27.1342
41 Male Prothrombin Complex Activity 120.0 26 32.08 11.7754 28.1411 36.0189
42 Male Prothrombin Complex Activity 144.0 8 34.2857 13.925 25.1308 43.4407

5 Plot of Summarized Observations Over Time

Re-create the following plot of the summarized PK and PD observations over time: