Multiple small improvement

[dlefaudeux]

• fix issue with resolution unit (closes fix outputSchema with resolution unit #92 )
• add plasma and plasma unbound as default outputs for both victim and perpetrator (closes Add plasma unbound and total as default outputs for victim #94 Show perpetrator to in results/plots #101)
• add victim only simulation as default (closes Add victim only simulation #58)
• improve help of formulation (closes Improve help of create_formulation indentation of list #89)
• create/add individuals from osp.snapshots (closes Add/Create new individuals #113)

[nautilus69]

1- #' @param individual_name name(s) of the formulation(s) to remove
Should say "individual(s)", not "formulation(s)".

2- Missing NULL fallback in resolution switch() (R/outputSchema.R:34-54)

Both switch() calls in the data active binding have no default case. If x$unit is a valid time unit not covered
(e.g., "ms" — milliseconds is a valid ospsuite time unit), the switch() silently returns NULL, which would produce
malformed JSON output.

3- Resolution conversion logic may be incorrect for week(s) (R/outputSchema.R:40) : The hardcoded parts require revisions

4. No validation on individual parameter in add_individual (R/snapshot.R:155) (I am not sure about old behavior)

5- tests for add-individual / remove_individual and for resolution unit conversion logic (for week and year)

The add_formulation method (via add_item) presumably validates the object type. But with the new wrapping of
individuals via Individual$new(), there's no check that the individual argument to add_individual() is actually an
Individual object. If a user passes raw list data (which was the old format), it would silently add invalid data.

[nautilus69]

1 & 2 + tests needed to be addressed,

the rest are optional for now.

[dlefaudeux]

2- Missing NULL fallback in resolution switch() (R/outputSchema.R:34-54)

Only schema with units in ospsuite::getUnitsForDimension("Time") can be added, switch list all possible units. Do I really need a fallback I feel like it should never be triggered

ms is not in ospsuite::getUnitsForDimension("Time")

[dlefaudeux]

3- Resolution conversion logic may be incorrect for week(s) (R/outputSchema.R:40) : The hardcoded parts require revisions

Why ?
I can use that below but I felt like it is putting overheads for nothing
x$resolution / ospsuite::toUnit("Time", 1, sourceUnit = "week(s)", targetUnit = "day(s)") instead of x$resolution / 7

same reason for "ks"

[Copilot]

Pull request overview

This PR bundles several small enhancements across the snapshot/simulation workflow: fixing output schema resolution unit handling, expanding default outputs (plasma + plasma unbound) for victim/perpetrator, adding a default “victim only” simulation template, improving formulation docs, and integrating osp.snapshots Individuals/Populations into Snapshot.

Changes:

• Adjust output schema resolution serialization to normalize certain time units (e.g., week/month/year/ks) and extend related tests/snapshots.
• Update generic simulation template + simulation initialization defaults to include Plasma Unbound outputs, and add a default “victim only” simulation.
• Wrap snapshot Individuals/Populations using osp.snapshots classes and add Snapshot$add_individual() / Snapshot$remove_individual() with documentation updates.

Reviewed changes

Copilot reviewed 19 out of 19 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
tests/testthat/test-snapshot.R	Adds a test around individual add/remove behavior.
tests/testthat/test-outputSchema.R	Updates interval snapshot expectations and adds resolution conversion tests.
tests/testthat/_snaps/simulation_template.md	Updates snapshot output for new template defaults (unbound + victim-only sim).
tests/testthat/_snaps/simulation.md	Updates printed simulation outputs to include Plasma Unbound selections.
tests/testthat/_snaps/run-simulations.md	Updates result snapshots reflecting new default outputs and messages.
tests/testthat/_snaps/outputSchema.md	Updates printed output schema snapshot for new interval example.
man/create_formulation.Rd	Restructures help content into clearer sections per formulation type.
man/add_observed_data.Rd	Fixes value description text for observed data helper.
man/Snapshot.Rd	Documents new add_individual / remove_individual methods.
man/DDI.Rd	Adds inherited method links for individual add/remove.
inst/extdata/generic_simulation_template.json	Adds Plasma Unbound outputs and a default “victim only” simulation.
R/snapshot.R	Converts Individuals/Populations to osp.snapshots R6 objects; adds add/remove individual methods; updates export.
R/simulations.R	Initializes simulations with default Plasma + Plasma Unbound output selections.
R/outputSchema.R	Converts resolution value/unit for specific time units when exporting schema JSON.
R/formulation.R	Improves roxygen help structure for create_formulation().
R/ddi.R	Switches individual name lookup to the new individual representation ($name).
R/cts-package.R	Adds new osp.snapshots imports.
NAMESPACE	Adds osp.snapshots importFrom entries.
DESCRIPTION	Adds osp.snapshots to Imports and lists it under Remotes.

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[Copilot]

These @importFrom osp.snapshots ... entries appear unused in the package code (AdvancedParameter and create_individual are not referenced anywhere under R/). Keeping unused imports can trigger R CMD check notes and makes the dependency surface larger than necessary. Consider removing the unused imports (and the matching NAMESPACE entries) or using them via unqualified calls if they’re intended to be part of the public API.

Suggested change

	#' @importFrom osp.snapshots AdvancedParameter
	#' @importFrom osp.snapshots create_individual

[dlefaudeux]

They are not used but I want them to be usable by the user directly.