inst/doc/analysis-plan-governance.R

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

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

## ----eval=requireNamespace("openssl", quietly=TRUE)---------------------------
plan <- declare_gazepoint_analysis_plan(
  research_question =
    "Can predefined recording-quality review status generalize to new participants?",
  scientific_purpose =
    "Evaluate a predefined, observed recording-quality endpoint.",
  outcome = "quality_status",
  outcome_definition = "Predefined observed QC review label.",
  predictors = c("fixation_duration", "pupil_change"),
  generalization_target = "new_participants",
  grouping_variables = "participant_id",
  eligible_population = "Participants meeting the study protocol.",
  preprocessing_plan = "Fit preprocessing only inside each analysis partition.",
  candidate_models = c("glm", "ranger"),
  primary_metric = "balanced_accuracy",
  secondary_metrics = c("sensitivity", "specificity"),
  calibration_metric = "brier",
  uncertainty_method = "participant_cluster_bootstrap",
  threshold_policy = "Select only within inner resampling.",
  external_validation_required = TRUE,
  seed_strategy = "Predeclared deterministic seeds."
)

locked <- lock_gazepoint_analysis_plan(plan)
locked$plan_id