Getting Oriented in R

Set up a confident, reproducible R workflow for pharmacometrics: RStudio/Positron basics, scripts, projects, and the PMx mindset.
Tip

Big idea: In PMx, your goal is not “run code once.” Your goal is reproducible analysis that you (or someone else) can rerun later with confidence.

Before You Start: Install R and an IDE

You need two things:

1. Install R (the language)

Download R from CRAN:

Choose your operating system and install.

2. Install an IDE (your workspace)

You have two excellent options from Posit:

Note

R is the engine.
RStudio or Positron is the dashboard.

Learning Objectives

By the end of this lesson, you will be able to:

  • Describe what R is used for in PMx workflows (wrangling → visualization → modeling → reporting).
  • Navigate the RStudio or Positron interface (Script/Source, Console, Environment, Plots/Viewer).
  • Run code from a script (not just the Console) and explain why that matters.
  • Use an RStudio/Positron Project (.Rproj) to keep paths and files organized.
  • Adopt a “PMx mindset” for clean, auditable, reproducible work.

Key Ideas

R vs RStudio vs Positron (don’t mix them up)

  • R is the programming language (it runs your code).
  • RStudio is an IDE (a workspace that makes R easier to use).
  • Positron is a modern IDE from Posit that also supports R workflows and projects.

If R is an engine, RStudio/Positron is the dashboard.

Why scripts matter in PMx

Typing commands in the Console is fine for quick checks.
But PMx work should live in scripts so you can:

  • rerun analyses end-to-end
  • share work with collaborators
  • review changes (version control)
  • avoid “it worked yesterday” problems

Your IDE Tour (5 minutes)

When you open RStudio or Positron, you usually see panes like these:

  1. Source (Script editor): where you write .R scripts or .qmd files
  2. Console: where code executes
  3. Environment / History: what objects exist in memory
  4. Plots / Files / Packages / Help / Viewer: output and navigation

Rstudio Layout

Positron Layout
Note

If your layout looks different, that’s okay. The important part is knowing where code is written (Source) vs executed (Console).

Running Code the “Right” Way

Create a script (File → New File → R Script), then try this:

x <- 2 + 3
x

Run using:

  • Cmd/Ctrl + Enter

You should see:

[1] 5

Why not just type everything in the Console?

Because the Console is temporary. A script is repeatable.

The PMx Workflow Loop

In pharmacometrics, you will repeatedly:

  1. Load data
  2. Inspect + QC
  3. Wrangle
  4. Visualize
  5. Model
  6. Report/export

Projects (.Rproj)

An RStudio Project is a folder that contains a .Rproj file.

Both RStudio and Positron can open .Rproj files. When you open a project:

  • The project folder becomes the working directory
  • Files are organized in a consistent location
  • Relative paths work reliably across machines
Note

Positron can also work directly with plain folders. However, using a .Rproj project keeps workflows consistent with RStudio and with most R-based PMx teams.

Tip

Use relative paths like:

read.csv("data/myfile.csv")

Avoid absolute paths like /Users/yourname/Downloads/...

Your First Reproducibility Header

# Course: R for Pharmacometrics
# Lesson: R Basics 01
# Purpose: Getting oriented and setting up reproducible workflow
# Author: Your Name
# Date: 2026-02-21
Note

In R, the # symbol starts a comment.
Comments are ignored by R and are for humans reading the code.

Practice Problems

  1. Create a script and run 2 + 2 from the script.
  2. Create id <- 101 and print it.
  3. Restart R. What happens?
  4. Create a Project for this course.
  5. Write one sentence explaining why scripts matter in PMx.

1–2. Run code from a script

2 + 2
[1] 4
id <- 101
id
[1] 101

3. Restart R

After restarting, objects in the Environment disappear. That’s expected—and it’s why scripts matter.

4. Create a Project

In RStudio:

  • File → New Project → Existing Directory (or New Directory)
  • Choose your course folder
  • Open the .Rproj file to work in that project

5. One-sentence PMx reason

Example:

“Scripts make my analysis reproducible and auditable, which is essential in PMx work.”

Summary

  • R is the engine.
  • RStudio and Positron are workspaces.
  • Scripts ensure reproducibility.
  • Projects keep paths stable.
  • PMx analysis follows a structured workflow loop.
  • If something “mysteriously breaks,” restart R and rerun the script top-to-bottom.
  • Prefer projects + relative paths.
  • Keep a clean folder structure from day 1.
  • Save your work often, and use version control when you’re ready.