Why English? | Making TRIPOD-Code Repositories Reproducible Through Dependencies, Licences, Tests, Workflows, Archives and Reuse

ORIENTATION

What this guide owns

Current fact check

The EQUATOR record places development, validation and updating of multivariable diagnostic or prognostic models within scope, using statistical or machine-learning methods. The 2026 protocol describes five development stages and separates code sharing from sharing trained model artefacts. A 2026 scoping review was published to inform the project by assessing current code-sharing practice.

Canonical boundary

This article owns code-repository reporting and computational reproducibility for prediction-model studies under TRIPOD-Code. TRIPOD-P owns study protocols, TRIPOD+AI owns the research report more broadly, and general software-engineering guidance owns code quality beyond minimum research reporting.

Worked example

Every chapter returns to a fictional hospital team publishing code for a model that predicts 30-day readmission from routinely collected admission data. It is fictional, low-stakes and educational; it does not report a real school, clinical decision or guaranteed outcome.

Warm up with eduKate’s guides to explaining scientific evidence and asking better questions in class.

CHAPTER 1 OF 16

1. State the Repository’s Purpose and Scope

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Why this move matters

Explain which paper, analysis, model stage and outputs the repository covers, plus deliberate exclusions.

Connect prose to executable artefacts

Explain which paper, analysis, model stage and outputs the repository covers, plus deliberate exclusions. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: The repository recreates preprocessing and external validation but not protected data extraction. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

A complete scope statement cannot fill missing code. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “State the Repository’s Purpose and Scope”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

CHAPTER 2 OF 16

2. Map Every Claim to Code

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Why this move matters

Link figures, tables, model estimates and metrics to scripts, notebooks, configuration and execution order.

Connect prose to executable artefacts

Link figures, tables, model estimates and metrics to scripts, notebooks, configuration and execution order. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: A result map shows that table 2 comes from validate.py with config/external.yaml. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

A link can point to code that no longer matches the published run. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “Map Every Claim to Code”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

CHAPTER 3 OF 16

3. Describe Inputs and Data Contracts

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Why this move matters

Define expected files, columns, types, units, coding, missing values, inclusion filters and synthetic examples.

Connect prose to executable artefacts

Define expected files, columns, types, units, coding, missing values, inclusion filters and synthetic examples. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: A schema explains admission time, diagnosis codes and the readmission outcome without releasing patient rows. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

A synthetic example may not reproduce real data complexity. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “Describe Inputs and Data Contracts”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

CHAPTER 4 OF 16

4. Document Preprocessing and Leakage Controls

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Why this move matters

Show cleaning, feature creation, time windows, imputation, splitting and safeguards against using future information.

Connect prose to executable artefacts

Show cleaning, feature creation, time windows, imputation, splitting and safeguards against using future information. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: The code splits by admission date before fitting the imputer. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

Visible code does not prove the same steps were used for the paper. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “Document Preprocessing and Leakage Controls”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

CHAPTER 5 OF 16

5. Freeze the Computational Environment

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Why this move matters

Report operating system, language, package versions, hardware or accelerators, random seeds and installation method.

Connect prose to executable artefacts

Report operating system, language, package versions, hardware or accelerators, random seeds and installation method. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: A lock file and container recipe recreate the tested environment. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

Containers may depend on external images or services that later disappear. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “Freeze the Computational Environment”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

CHAPTER 6 OF 16

6. Provide One Reliable Execution Path

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Why this move matters

Give ordered commands, working directory, configuration, resource needs, expected runtime and success output.

Connect prose to executable artefacts

Give ordered commands, working directory, configuration, resource needs, expected runtime and success output. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: A single make reproduce target rebuilds validation metrics from prepared inputs. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

One command can hide undocumented network calls or credentials. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “Provide One Reliable Execution Path”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

CHAPTER 7 OF 16

7. Explain File Structure and Modularity

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Why this move matters

Describe directories, entry points, shared functions, generated files and where users should or should not edit.

Connect prose to executable artefacts

Describe directories, entry points, shared functions, generated files and where users should or should not edit. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: README sections distinguish source, configuration, tests, examples and outputs. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

A tidy structure does not guarantee correct analysis. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “Explain File Structure and Modularity”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

CHAPTER 8 OF 16

8. Report Tests and Verification

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Why this move matters

Identify unit, integration, regression and data-validation tests, what each protects, how to run them and known gaps.

Connect prose to executable artefacts

Identify unit, integration, regression and data-validation tests, what each protects, how to run them and known gaps. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: A regression test compares external-validation metrics with archived expected values. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

Passing tests cover only encoded expectations. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “Report Tests and Verification”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

CHAPTER 9 OF 16

9. State Availability and Access Conditions

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Why this move matters

Give persistent repository location, access date, branch or tag, restrictions and contact route.

Connect prose to executable artefacts

Give persistent repository location, access date, branch or tag, restrictions and contact route. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: The paper cites a release tag and DOI rather than a moving default branch. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

Public access today does not guarantee long-term availability. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “State Availability and Access Conditions”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

CHAPTER 10 OF 16

10. Choose a Clear Licence

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Why this move matters

Name the software licence, third-party restrictions, data terms and what reuse, modification or redistribution is permitted.

Connect prose to executable artefacts

Name the software licence, third-party restrictions, data terms and what reuse, modification or redistribution is permitted. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: The repository uses a recognised open-source licence and separately explains non-shareable data. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

A permissive licence cannot override data law or upstream terms. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “Choose a Clear Licence”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

CHAPTER 11 OF 16

11. Separate Code From Model Artefacts

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Why this move matters

Report where fitted weights, coefficients, preprocessing objects, vocabularies or APIs are stored and how versions correspond.

Connect prose to executable artefacts

Report where fitted weights, coefficients, preprocessing objects, vocabularies or APIs are stored and how versions correspond. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: Code is public; the fitted model object has its own checksum and release record. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

A shared model artefact may still be unusable without the original feature pipeline. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “Separate Code From Model Artefacts”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

CHAPTER 12 OF 16

12. Provide Lawful Data Substitutes

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Why this move matters

When data cannot be shared, explain governance and offer schemas, synthetic data, simulated tests or controlled-access instructions.

Connect prose to executable artefacts

When data cannot be shared, explain governance and offer schemas, synthetic data, simulated tests or controlled-access instructions. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: A synthetic dataset exercises every branch without containing patient information. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

Synthetic data cannot establish performance on the protected population. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “Provide Lawful Data Substitutes”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

CHAPTER 13 OF 16

13. Version Code, Configuration and Outputs

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Why this move matters

Use tags, commit identifiers, change logs and checksums to connect the published analysis to exact artefacts.

Connect prose to executable artefacts

Use tags, commit identifiers, change logs and checksums to connect the published analysis to exact artefacts. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: The manuscript cites release v1.0.0 and the archived output checksum. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

A commit can depend on unversioned external data or services. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “Version Code, Configuration and Outputs”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

CHAPTER 14 OF 16

14. Archive for Long-Term Access

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Why this move matters

Deposit a release in a durable archive, record identifiers and retention limits, and avoid relying only on a personal account.

Connect prose to executable artefacts

Deposit a release in a durable archive, record identifiers and retention limits, and avoid relying only on a personal account. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: The release receives a DOI while development continues elsewhere. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

An archive preserves bytes, not necessarily an executable ecosystem. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “Archive for Long-Term Access”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

CHAPTER 15 OF 16

15. Record Execution, Failures and Deviations

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Why this move matters

Keep logs, environment capture, warnings, manual steps, failed runs and changes from the published plan.

Connect prose to executable artefacts

Keep logs, environment capture, warnings, manual steps, failed runs and changes from the published plan. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: The team records that one library patch changed numerical tolerance and reruns validation. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

A log may expose secrets or protected paths and needs careful redaction. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “Record Execution, Failures and Deviations”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

CHAPTER 16 OF 16

16. Conclude With a Reproducibility Claim

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Why this move matters

Distinguish inspectable code, runnable workflow, reproduced outputs and independently replicated findings.

Connect prose to executable artefacts

Distinguish inspectable code, runnable workflow, reproduced outputs and independently replicated findings. Link each analytical claim to the script, configuration, environment, input contract and output needed to reproduce it.

Rebuild one prediction result

Worked example: The repository supports independent execution on synthetic data and controlled replication on protected data. Start from the documented input, recreate the environment, run preprocessing, training or loading, validation and metric generation, then compare outputs.

Separate code, model and data access

State which repository holds analytical code, which artefact stores a fitted model, which data are shareable, and what lawful or practical substitute supports checking when data cannot be released.

Respect the development boundary

Shared code cannot guarantee correctness, transportability or clinical value. TRIPOD-Code is still being developed. The protocol and EQUATOR record describe intended reporting areas, not a final numbered checklist.

Student, parent and career transfer

Make one evidence card for “Conclude With a Reproducibility Claim”: source location, plain-language meaning, limit and next question. A parent or teacher can ask for one everyday explanation and one specialist explanation; both must preserve the same conditions. This habit supports data science, biostatistics, software engineering, clinical prediction, research methods, open science, model validation, health informatics and technical writing without promising a grade, admission, funding decision or job.

PRACTICE LAB

Build a tripod_code decision trail

Student route

1. Choose one original report inside this guide’s scope.
2. Copy its objective and underline actor, action, context, evidence and intended decision.
3. Draw the specific reasoning chain used in this article.
4. Mark each step reported, inferred, contested or unknown.
5. Rewrite the conclusion so it preserves the narrowest important limitation.

Parent or teacher route

Ask the learner to explain turn “code available” into instructions another researcher can actually inspect, run, verify and responsibly reuse twice: once to a classmate and once to a method specialist. Praise a precise correction and a well-stated unknown; both show disciplined attention to evidence.

Early-career route

Create a one-page tripod_code audit with source link, date checked, scope, method logic, decisive wording, contrary evidence, limit and next action. A colleague should be able to continue without guessing.

Continue with eduKate’s guides to reading course and career information and giving useful feedback in group projects.

USEFUL NEXT READING

Connect this narrow owner to its neighbour

Read the TRIPOD-P prediction-model protocol guide for a related but different reader job. Return here when the question is specifically how to turn “code available” into instructions another researcher can actually inspect, run, verify and responsibly reuse. This boundary keeps one canonical owner per intent.

For English practice across research, school and career communication, visit the English at work and in public life guide.

FREQUENTLY ASKED QUESTIONS

Questions students and parents often ask

What is TRIPOD-Code?

A developing TRIPOD extension for code repositories linked to diagnostic and prognostic prediction-model studies.

Is it final?

No. The checked sources describe the development protocol and intended reporting areas.

Does it cover model files?

It recognises model artefacts but treats model sharing as distinct from code sharing.

Why does a licence matter?

Access to code does not by itself grant permission to reuse or modify it.

Can protected data make reproducibility impossible?

Some result replication may require controlled access, but schemas, synthetic data, tests and transparent code can still support inspection.

Does passing tests prove the model is valid?

No. Tests show encoded behaviours; model validity requires separate evidence.