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Summary
Every pillar's uncertainty output is now expressible as the same
S3 object — edaphos_posterior — and admits the same
calibration diagnostic, plotting routine and adapter protocol.
Calibrating the six pillars against their natural ground truth now
takes three lines of code.
New core infrastructure
edaphos_posterior()— S3 class carrying either a
(n_samples, query_shape)sample array or a Gaussian
(mean, sd)summary, with pre-computed quantile fields, an
optional epistemic / aleatoric decomposition, a method tag
("ensemble" | "bootstrap" | "mcdropout" | "bayesian" | "loo_cv" | "analytic" | ...) and a query-type tag
("effect" | "map" | "sample" | "feature" | ...).uncertainty_calibrate()— single diagnostic returning CRPS
(Gini-mean-difference Monte-Carlo formula of Gneiting & Raftery
2007), PICP and MPIW at each requested nominal level, a
reliability data frame and the point RMSE.autoplot.edaphos_posterior()— ggplot2 dispatch on
query_type.uncertainty_plot_reliability()— reliability-diagram plot.as_edaphos_posterior()— S3 generic adapted to every pillar.
Per-pillar adapters
| Pillar | New API | Method |
|---|---|---|
| 1 | causal_effect_posterior(), causal_effect_bootstrap() |
cluster-block bootstrap (LM) / BART posterior |
| 2 | piml_neural_ode_posterior(), piml_bayes_posterior() |
K-seed deep ensemble / Laplace or MCMC |
| 3 | temporal_convlstm_ensemble_fit(), temporal_convlstm_ensemble_rollout(), temporal_convlstm_mcdropout_predict() |
K-seed ensemble / MC-dropout / Kalman analysis |
| 4 | foundation_finetune_ensemble(), foundation_mcdropout_predict() |
K-seed head ensemble / MC-dropout head |
| 5 | active_learning_posterior() |
QRF quantile grid |
| 6 | quantum_krr_posterior() |
GP-equivalent analytic posterior |
New vignette
vignette("uncertainty-unified") — compact end-to-end tour
through the six pillars with the same three-line recipe
(as_edaphos_posterior → uncertainty_calibrate → autoplot),
the single CRPS / PICP@95 / MPIW@95 / point-RMSE table that is
now the package's headline diagnostic, and a faceted reliability
diagram.
Deliverables
R/uncertainty.R— the core infrastructure (constructor,
calibration, autoplot dispatch, reliability plot, generic adapter).R/{causal,piml,temporal,foundation,active,quantum}_posterior.R
— one file per pillar with the adapter + pillar-specific posterior
helpers.tests/testthat/test-*-posterior.R— 126 new tests across
seven files.vignettes/uncertainty-unified.Rmd— the calibration-table
narrative.
Quality
- R CMD check: 0 errors / 0 warnings / 1 unrelated NOTE
(future file timestamps — system-clock artefact). - Backwards compatible: no existing API was renamed or removed;
every new entry point is additive.