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Convert a snapshot collection to a tibble or list of tibbles

as_tibbles.Rd

Unified bridge from a Snapshot to the tidyverse for any building-block kind plus observed data. Replaces the nine per-kind get_*_dfs() functions as the canonical entry point; those remain available as thin wrappers. Omit kind to convert every kind of a snapshot in a single call.

Usage

as_tibbles(snapshot, kind = NULL)

Arguments

snapshot

A Snapshot object.

kind

Character vector naming the collection(s) to convert, or NULL (the default) to convert every kind. Each element must be one of "compounds", "individuals", "formulations", "populations", "events", "expression_profiles", "protocols", "observer_sets", "observed_data". A length-1 kind returns that kind's native shape directly (a tibble or a named list of tibbles); a length-2-or-more kind returns a named list keyed by the requested kinds, in request order; NULL returns a named list of all nine kinds in the order above.

Value

When kind names a single collection, a tibble or a named list of tibbles for that collection (see below). When kind names several collections, or is NULL (all nine kinds), a named list keyed by the requested kinds, each entry the native shape of that kind:

  • "compounds": a list with properties and processes tibbles. properties carries one row per (compound, physicochemical property) pair (plus folded process rows for backwards compatibility); processes is the long-form, one row per (compound, process, parameter) triple.

  • "protocols", "observed_data": a single tibble.

  • "observer_sets": a list with observer_sets (one row per ObserverSet) and observers (one row per Observer, joinable to its parent via observer_set_id / observer_set_name).

  • "individuals": a list with individuals, individuals_parameters, individuals_expressions.

  • "formulations": a list with formulations, formulations_parameters.

  • "populations": a list with populations, populations_parameters.

  • "events": a list with events, events_parameters.

  • "expression_profiles": a list with expression_profiles, expression_profiles_parameters.

Examples

if (FALSE) { # \dontrun{
snapshot <- load_snapshot("Midazolam")

# List of tibbles (compounds returns properties + processes)
compounds <- as_tibbles(snapshot, "compounds")
compounds$properties
compounds$processes

# List of tibbles
individuals <- as_tibbles(snapshot, "individuals")
individuals$individuals_parameters

# Omit `kind` to convert every kind at once, keyed by kind name
all_kinds <- as_tibbles(snapshot)
names(all_kinds)
} # }