inst/doc/external-validation-reporting.R

In gp3ml: Governance-First Predictive Modelling for 'Gazepoint' Research

## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
options(gp3ml.reproducible_examples = TRUE)
library(gp3ml)

## ----development--------------------------------------------------------------
development <- simulate_gazepoint_governed_data(18L, 6L, 1L, seed = 2901L)
predictors <- c("tracking_ratio", "blink_rate", "gaze_dispersion")
task <- create_gazepoint_synthetic_task(development, "recording_quality", "new_participants")
manifest <- create_gazepoint_synthetic_manifest(task$outcome, predictors)
folds <- create_gazepoint_group_folds(
  development, task$outcome, predictors, manifest,
  task$generalization_target,
  "participant_id", "trial_id", "stimulus_id",
  v = 3L, repeats = 1L, seed = 2901L
)
development_evaluation <- evaluate_gazepoint_group_folds(
  folds, task, predictors, "glm", seed = 2901L,
  assess_calibration = TRUE, calibration_bootstrap = 0L
)
model <- fit_gazepoint_model(
  development, task, predictors, "glm", seed = 2901L
)

## ----external-----------------------------------------------------------------
external <- simulate_gazepoint_governed_data(10L, 6L, 1L, seed = 2902L)
external$participant_id <- paste0("E", external$participant_id)
external$trial_id <- paste0("E", external$trial_id)
external$stimulus_id <- paste0("E", external$stimulus_id)
declaration <- declare_gazepoint_external_dataset(
  external,
  label = "synthetic_external_site",
  independent = TRUE,
  origin = "Independent deterministic synthetic generation"
)
report <- evaluate_gazepoint_external_transportability(
  model,
  development_data = development,
  external_data = external,
  declaration = declaration,
  development_evaluation = development_evaluation,
  bootstrap = 0L,
  seed = 2902L
)
report
report$performance_comparison
report$group_coverage

## ----absent-------------------------------------------------------------------
not_validated <- evaluate_gazepoint_external_transportability(
  model,
  development_data = development,
  external_data = NULL
)
not_validated