Agentic Coding ("Vibe Coding") - The Dark Side of the Moon?

C O D I N G S U B G R O U P · O N B O A R D I N G
Agentic Coding
(“Vibe Coding”)
The Dark Side of the Moon?
Ben Geisler

2
P A R T 0 1
Speak to Me
We hit enter
0:00 – 0:05

3
P A R T 0 2
Time
Playlist
0:05 – 0:07

0 2 · T I M E
4
Playlist
01 Speak to Me 0:00 – 0:05
Fired the prompt
02 Time 0:05 – 0:07
Playlist
03 Breathe (In the Air) 0:07 – 0:12
Why bother — Paul Schneider
04 Us and Them 0:12 – 0:15
Three modes of AI-assisted coding
05 On the Run 0:15 – 0:21
Back to the IDE
06 The Great Gig in the Sky 0:21 – 0:28
Did it get the right answer?
07 Any Colour You Like 0:28 – 0:34
The tech stack
08 Money 0:34 – 0:41
Accounts, installing, where things live
09 Breathe (Reprise) 0:41 – 0:46
CLAUDE.md
10 Brain Damage 0:46 – 0:54
Skills, plugins, MCPs — and validateHE
11 Eclipse 0:54 – 1:00
Close

5
P A R T 0 3
Breathe (In the Air)
Why bother? Over to Paul Schneider
deck.shoulde.rs/using-ai-in-july-2026
0:07 – 0:12

6
P A R T 0 4
Us and Them
Three modes of AI-assisted coding
0:12 – 0:15

0 4 · U S A N D T H E M
7
Three Modes of AI-Assisted Coding
Autocomplete
AI suggests the next line as you type
GitHub Copilot • Cursor Tab •
Codeium • Tabnine
Fastest adoption. Works inside the editor,
filling boilerplate and completing patterns.
The “spellcheck” of coding.
Chat / Copy-Paste
Ask a question, get code back
ChatGPT • Claude.ai • Gemini • Perplexity •
GLM • Kimi • Qwen • DeepSeek
Most familiar mode. Describe a problem in
natural language, copy the response into
your project. High flexibility, low integration.
Agentic Coding
AI reads your codebase, plans, writes across files
— and runs them
Claude Code • Codex • Cursor Agent •
Windsurf • Antigravity
Newest and most powerful. Operates like a
junior developer — reads context, makes
multi-file changes, runs the code. This is
what is running behind me.

0 4 · U S A N D T H E M
8
Agents: What’s Actually Different?
Four things — and the middle two are the ones that matter later
1 It sees the whole project
Not the snippet you pasted. It has just read a thirty-page
PDF that I never opened.
2 It runs the code — and changes it
Errors go straight back to it, not through you. It edits the
file, runs it again.
3 It keeps going until the result is right
Given a definition of “done” — no errors, outputs non-
empty, a table in the shape of the paper’s — it iterates
until it gets there.
4 It works while you don’t
Which is why there is a stopwatch running behind this
slide.

9
P A R T 0 5
On the Run
Back to the IDE
0:15 – 0:21

10
P A R T 0 6
The Great Gig in the Sky
Did it get the right answer?
0:21 – 0:28

0 6 · T H E G R E A T G I G I N T H E S K Y
11
Paper vs. Rebuild
Lund et al. 2022, Stroke — cost-effectiveness of Mobile Stroke Unit care in Norway
What we compare
Lifetime cost per patient, MSU and standard care
Incremental cost
Incremental QALYs
ICER
(PSA)
L U N D 2 0 2 2
The model
Decision tree for the acute phase, then a 3-state Markov:
independent (mRS 0–2), dependent (mRS 3–5), dead.
Annual cycle · 25-year horizon · 4% discount on costs and
QALYs · 2021 NOK · Norwegian health-service perspective.
Then, before anyone asks: what it got wrong.
Lund UH, Stoinska-Schneider A, Larsen K, Bache KG, Robberstad B. Stroke 2022;53(10):3173–81. doi:10.1161/STROKEAHA.121.037491

12
P A R T 0 7
Any Colour You Like
The tech stack
0:28 – 0:34

0 7 · A N Y C O L O U R Y O U L I K E
14
Pick an IDE— Any One
R itself does not change. Claude Code calls Rscript with the R and the packages you already have.
M A D E B Y P O S I T
RStudio
What you use today. Claude Code runs in the Terminal pane
— nothing to install in the editor itself.
M A D E B Y P O S I T · R E C O M M E N D E D
Positron
RStudio’s successor from the same company: same panes,
same feel, plus VS Code extensions — including Claude
Code.
M I C R O S O F T
VS Code
The most widely used editor there is. R and Quarto via two
extensions. Most guides assume it.
N O E D I T O R
Just a terminal
Claude Code and Rscript, nothing else. Works — which
shows the editor is a convenience, not a requirement.

0 7 · A N Y C O L O U R Y O U L I K E
15
What Else You Need
Three things, each installed once
V E R S I O N C O N T R O L A N D B A C K U P
Git + GitHub
Git records every version of your work locally; GitHub keeps a
copy online and lets you share it. gh (the GitHub CLI) handles the
login.
Git for Windows · GitHub
CLI · free GitHub account
T H E A G E N T
Claude Code or
GPT/Codex (or sth. else)
Runs in any terminal — including RStudio’s — and as an extension
in Positron and VS Code. Reads your project, runs Rscript, edits
files.
One installer · Claude
account (Pro or Max)
I N T H E E D I T O R
R and Quarto support
Syntax, running code, .qmd reports. Built into RStudio and
Positron; two extensions in VS Code.
Nothing to do in RStudio /
Positron

16
P A R T 0 8
Money
Accounts, installing, where things live
0:34 – 0:41

0 8 · M O N E Y
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What It Costs
Pick one of the three — plus GitHub, which is free
Claude
Anthropic
Free no Claude Code
Pro $20 / month (Fable not included)
Max $100 – 200 / month
GPT (ChatGPT/Codex)
OpenAI
Free/Go $0 / month; very limited
Plus $20 / month
Pro $100 – 200 / month
GLM Coding Plan
Z.ai (Zhipu), China
Lite $10 / month
Pro $30 / month
Max $80 / month
A cheaper model that plugs into Claude
Code. Kimi and Qwen are similar.
Another alternative: free local model
(requires strong GPU)
GitHub Free — unlimited private repositories. Enough for everything today.

0 8 · M O N E Y
18
Installing on a University (or Enterprise) Machine
UiO, EUR — no admin rights needed for most of it
1 The IDE
VS Code, R and Git are usually in the Company Portal / Software Center already — a few clicks, no ticket. Positron installs into
your user directory, no admin rights at all.
2 Claude Code / Codex extension
Installs into your user profile. Use the extensions menu within VS Code or Positron (Codex not available for Positron)
3 Git for Windows
Company Portal / Software Center.
Most of this is a few clicks. Anything that is not is a short ticket to IT, not a project.

0 8 · M O N E Y
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One-Time Setup — About Five Lines
You do this once, ever
git config --global user.name "Your Name"
git config --global user.email "you@uio.no"
gh auth login
gh repo create my-model --private --source=. --push
“SSH keys” sounds like systems administration. gh auth login does the whole thing in a browser window — choose SSH when
it asks and it makes and uploads the key for you. You never think about it again.
If you get stuck, just “ChatGPT” it!

0 8 · M O N E Y
20
Where to Put the Folder
C:Users<you>git<project> not OneDrive/Sharepoint, Dropbox, or Google Drive
1 Git and sync clients do not mix
Both try to manage the same files. You end up with analysis (1).R and analysis (2).R.
2 GitHub is the backup
And the full history. Once the project is on GitHub, the sync folder has nothing left to do.
3 On UiO machines, Documents and Desktop already sync to OneDrive
So, make one separate git folder for all your projects in the main user directory and keep it there.

0 8 · M O N E Y
21
How to Structure the Project Folder
What the coding subgroup agreed — Paul calls it “making your project legible to AI”
rprojecthome/
├── data/
│ ├── raw/
│ ├── tidy/
│ ├── sensitive/ # .gitignore
│ └── output/
├── scripts/
│ ├── R/
│ │ ├── analysis/
│ │ ├── functions/
│ │ └── tests/
│ └── QMD/
│ ├── report/
│ ├── technical_docs/
│ └── vignettes/
├── figs/
├── tables/
└── references/
data/
raw/ is what you received and is never edited. tidy/ is the cleaned version your scripts use.
sensitive/ is anything with a person in it — it never leaves the machine. output/ is model
results.
scripts/
R/analysis/ runs the model; R/functions/ is reusable code; R/tests/ checks it. QMD/ holds the
Quarto documents: the report, the technical documentation, worked examples.
figs/, tables/, references/
What goes in the paper, plus the .bib and .csl files Quarto needs to build it.
Why a convention now matters more
The agent stops guessing where things go, and one CLAUDE.md works for every project you
have.

22
P A R T 0 9
Breathe (Reprise)
CLAUDE.md — say it once, it repeats
0:41 – 0:46

OUTDATED
0 9 · B R E A T H E ( R E P R I S E )
23
Anatomy of the Prompt
What I did in February
“Imagine you are a senior health economist expert in…” Role
“…the paper in paper/paper.pdf…” Point at the inputs
“…rebuild the model in a new subdirectory R…” Task
“…XLSX tables and PDF figures; run until no errors and outputs non-
empty…”
Details — the definition of done
“Ultrathink…” Keyword
“…imagine your CTO is watching like a hawk; this needs to be one-shot.” Putting extra pressure on the model 😂

0 9 · B R E A T H E ( R E P R I S E )
24
CLAUDE.md — Write It, or Have It Written
A markdown file at the root of the project, read automatically at the start of every session
P L A I N M A R K D O W N
Option A — write it yourself
Thirty to sixty lines of plain text: where R is on this machine, how to
run things, package management, the folder layout, house
conventions, what “done” means, what not to do.
W H AT I D I D
Option B — let Claude Code write it
It has just read your whole project and knows the layout better than
you can be bothered to type. You edit for judgement, not for content
— about five minutes.

25
P A R T 1 0
Brain Damage
Skills, plugins, MCPs — and validateHE
0:46 – 0:54

1 0 · B R A I N D A M A G E
26
Four Words You Will Keep Hearing
In plain language
CLAUDE.md
The note on the fridge
Standing instructions for this project. Read every time, so you
never repeat yourself.
Skill
A recipe
Step-by-step instructions, plus any scripts they need, that it
follows when you ask for that task. Written in plain
markdown.
Plugin
A recipe box you can share
A bundle of skills the whole group installs, so everyone
follows the same checklist.
MCP
An adapter
Lets it talk to things outside your folder — a database, Zotero,
a registry, a website.

27
validateHE — Five Modules
The ISPOR-SMDM Task Force-7 validation types, each one a module you can ask for
1 Transparency Is it documented well enough to review? Plus all 28 CHEERS 2022 items when there is a manuscript.
2 Face validity
A six-lens simulated council — clinician, modeller, health economist, HTA assessor, patient rep, payer —
who deliberate, with dissent recorded.
3 Verification
Does the code do what the modellers intended? Black-box perturbation tests, white-box line review, coding
standards.
4 Cross-validation Do other models of the same decision problem reach compatible answers?
5 External validation Does it reproduce what actually happened — life tables, registries, trial data?

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The Tests Every Modeller Means to Write
Module 3 derives these from first principles and runs them against your model
utilities = 1 → QALYs must equal life-years
costs = 0 → no costs accumulate
discount rate = 0 → discounted equals undiscounted
swap two strategies → results must swap
mortality = 0 → life-years equal the time horizon
double the effect → roughly double the incremental effect
cohort conservation · absorbing-state monotonicity · tunnel-state flow · determinism
on re-run

29
A Skill Is Just a Folder
Markdown, R scripts and a report template — nothing you could not open and read
validate-he/
├── SKILL.md
├── references/
│ ├── module-1-transparency.md
│ ├── module-2-face-validity.md
│ ├── module-3-verification.md
│ ├── module-4-cross-validation.md
│ ├── module-5-external-validation.md
│ └── checklist-routing.md
├── scripts/
│ ├── invariants.R
│ ├── blackbox_harness.R
│ ├── inventory.R
│ └── env_manifest.R
└── templates/
├── report_template.md
└── prompts/
SKILL.md
The workflow, in plain English: what to do, in which order, with what. This
is what Claude Code reads when you type /validate-he.
references/
The checklists and the protocol for each module — ISPOR-SMDM, TECH-
VER, AdViSHE, CDA-AMC, CHEERS, as markdown.
scripts/
Base R. The invariant checks, the perturbation harness, the function
inventory. Run inside a scratch copy of your model.
templates/
The Quarto skeleton for the report, and the prompts for each reviewer
role.

30
The Report
We can open one of these — and decide together which one
O P T I O N 1
Today’s rebuild
The Lund model Claude Code
just built
O P T I O N 2
UC2
ASCERTAIN CAR T-cell CEA
core model (PSM)
O P T I O N 3
UC3
NGS diagnostics core model
(decision tree)
O P T I O N 4
METIMMOX
My own model — just prior to
submission
What is in it
Executive summary — written for someone with no health economics and no programming
Technical body — every test with inputs, expected and observed; the completed checklists
Appendix A — recommended changes with file:line and severity. Not applied.
.install.ps1
/validate-he <model-folder>
--module 3
# needs R + Quarto on PATH

31
P A R T 1 1
Eclipse
Close
0:54 – 1:00

1 1 · E C L I P S E
32
Three Things to Take Away
1 The mode matters more than the model
You’ve been using chat. Agentic is a different tool, not a better chatbot.
2 Setup is one evening
Mostly one-time, and mostly no admin rights needed.
3 Verification is the job
The agent writes the code. You own whether it is right (or not).

1 1 · E C L I P S E
33
“The binding constraint on AI adoption is not technological,
it is experiential.”
– Paul Schneider
(which is why we are in a Zoom together, and not on a mailing list)

1 1 · E C L I P S E
34
Start Here This Week
In this order
1 Install Git and link it to GitHub
Git for Windows, a free GitHub account, gh auth login.
2 Install an IDE
Positron or VS Code via Company Portal / Software Center
3 Install Claude Code extension
plus the R / Quarto extensions if you chose VS Code
4 Create or clone a repo, open folder in IDE
In C:Users<you>git. Populate it with the folder structure.
5 Protect your data
data/sensitive/ goes in .gitignore before anything else
happens.
6 Create CLAUDE.md
Or ask Claude Code to write it, then edit it down. Then: point it
at a model you already have and ask it to explain the code back
to you.

36
B A C K U P
Questions I Expect
What about sensitive data?
Build and validate on synthetic or published data; run on the real thing only where policy allows.
data/sensitive/ in .gitignore is the concrete half of the answer.
What does it cost?
Pro is $20 / month, Max $100–200. The free plan does not include Claude Code. Codex currently not
supported in Positron.
Will it invent parameters? Yes, if you let it. Parts 06 and 10.
Do I have to give up RStudio? No — you can run it in parallel.
How is this different from Copilot? Part 04. Although Copilot might come out with agents itself.
Can it handle my 4,000-line model? Yes. That is closer to its strength than a blank folder.

Agentic Coding ("Vibe Coding") - The Dark Side of the Moon?