create_pathofmpred_object: Build a portable PathoFMPred model collection

In PathoFMPred: Tumour Feature Models from Pathology Representations

Build a portable PathoFMPred model collection

Description

Feature and outcome tables are linked only through 'id_column'. Outcome IDs must be unique. Feature IDs may repeat, for example when a patient has more than one slide, and are pooled before model development.

Usage

create_pathofmpred_object(
  feature_table,
  outcome_table,
  id_column,
  aggregation = c("mean", "median"),
  foundation_model = "custom",
  feature_columns = NULL,
  outcome_columns = NULL,
  outcome_types = NULL,
  positive_class = NULL,
  control = pathofmpred_control(),
  output_file = NULL
)

Arguments

feature_table	Data frame, matrix, or CSV path containing identifiers and numeric foundation-model features.
outcome_table	Data frame or CSV path containing one unique row per identifier and one or more outcomes.
id_column	Name of the identifier column present in both tables.
aggregation	How repeated feature rows are pooled: 'mean' or 'median'.
foundation_model	Label stored in the resulting object.
feature_columns	Optional numeric feature columns. By default all columns except 'id_column' are used.
outcome_columns	Optional outcomes to fit. By default all columns except 'id_column' are considered.
outcome_types	Optional named character vector containing 'continuous' or 'binary'. Otherwise numeric two-level outcomes are binary and other numeric outcomes are continuous.
positive_class	Event-class label for binary outcomes. Supply either one value when fitting a single binary outcome or a named character vector keyed by endpoint. Zero/one and FALSE/TRUE outcomes default to one and TRUE; all other binary labels require an explicit value.
control	Settings created by [pathofmpred_control()].
output_file	Optional '.rds' destination.

Value

A 'PathoFMPredObject' containing fitted models, a registry, nested-CV summaries, and a linkage/missingness audit.

PathoFMPred documentation built on Nov. 12, 2026, 5:10 p.m.