leafwax: Bayesian Calibration of Leaf Wax Hydrogen Isotope Reconstructions

The leafwax package provides tools for probabilistic inversion of leaf wax hydrogen isotope measurements (delta-2-H) to reconstruct precipitation isotope values. It integrates an explicit proper reconstruction prior with the likelihood under paired draws from hierarchical calibration posteriors.

Main Functions

invert_d2H: Bayesian inversion of leaf wax delta2H to precipitation delta2H
available_models: List all available calibration models
load_posteriors: Load posterior distributions for a specific model
get_model_parameters: Get model capabilities and required parameters
validate_model_inputs: Validate inputs for a specific model

Available Models

The package can inspect 14 calibration models with different capabilities. The The fitted variants include precipitation amount (baseline_env* and full* variants), C4 abundance, and PFT cover. Runtime capability flags in load_posteriors() are derived from each model's posterior columns at load time. The validated inversion interface currently supports only baseline, baseline_sp, and c4_only_sp; other designs fail closed because their complete new-site predictor basis is unavailable.

Basic models: baseline, baseline_sp
Precipitation models: baseline_env, baseline_env_sp
Vegetation models: baseline_veg, baseline_veg_sp, c4_only_sp
Combined spatial models: elevation_only_sp, elevation_c4_sp, elevation_c4_interact_sp
Full models: full, full_sp, full_interact, full_interact_sp

Models with "_sp" suffix use spatial Gaussian processes with 125 knots on a Fibonacci sphere lattice for improved uncertainty quantification.

Model Selection

Pass model = "auto" to predict_d2h_precip() to choose between the supported spatial baseline and C4-only designs. Model ensembles have no scientific default and must be supplied explicitly.

Key Features

Explicit proper reconstruction priors
Joint multi-row calibration-draw reweighting
Spatial correlation via Gaussian processes
No slope division, clipping, or post-hoc draw removal

References

Bowen, G. J., Cai, Z., Fiorella, R. P., & Putman, A. L. (2019). Isotopes in the water cycle: Regional-to global-scale patterns and applications. Annual Review of Earth and Planetary Sciences, 47, 453-479. doi:10.1146/annurev-earth-053018-060220

Sachse, D., Billault, I., Bowen, G. J., Chikaraishi, Y., Dawson, T. E., Feakins, S. J., ... & Kahmen, A. (2012). Molecular paleohydrology: Interpreting the hydrogen-isotopic composition of lipid biomarkers from photosynthesizing organisms. Annual Review of Earth and Planetary Sciences, 40, 221-249. doi:10.1146/annurev-earth-042711-105535

Author

Maintainer: Alexander S. Bradley abradley@wustl.edu (ORCID)

Examples

  # List available models
  models <- available_models()
  n_models <- length(models)

  # Priors are explicit; this constructor does not run an inversion.
  prior <- d2h_prior_normal(mean = -70, sd = 30)