Science Reference

Science Reference#

This section documents the scientific methods, QC thresholds, and validation bounds used by palmwtc.

Pipeline overview#

raw cycles ──► QC ──► flux ──► windows ──► validation
              │
              └── 30-min weather + soil + tree biophysics

Each stage is described in detail in the corresponding tutorial notebook under tutorials/. The integrated end-to-end run is covered in tutorials/000.

Method references#

  • Whole-tree-chamber method: Medlyn, B. E. et al. (2016). Pinpointing drivers of widespread declines in Australian streamflow. Global Change Biology, 22(8), 2834–2851.

  • CO₂ flux closure (Amax bounds): literature canopy-basis Amax 15–35 µmol m⁻² ground s⁻¹ (Lamade & Bouillet 2005).

  • Q10 respiration: 1.4–2.5 (literature range, tropical canopy).

  • Stomatal conductance (Medlyn g₁): Medlyn, B. E. et al. (2011). Reconciling the optimal and empirical approaches to modelling stomatal conductance. Global Change Biology, 17(6), 2134–2144. https://doi.org/10.1111/j.1365-2486.2010.02375.x

  • Isolation Forest (ML-assisted QC): Liu, F. T., Ting, K. M., & Zhou, Z.-H. (2008). Isolation forest. 2008 Eighth IEEE International Conference on Data Mining, 413–422. https://doi.org/10.1109/ICDM.2008.17

  • Breakpoint detection (PELT): Truong, C., Oudre, L., & Vayatis, N. (2020). Selective review of offline change point detection methods. Signal Processing, 167, 107299. https://doi.org/10.1016/j.sigpro.2019.107299

  • PAR conversion (shortwave → photosynthetic photon flux density): McCree, K. J. (1972). Test of current definitions of photosynthetically active radiation against leaf photosynthesis data. Agricultural Meteorology, 10, 443–453.

For the full per-function citation, see the docstrings on the implementing functions in palmwtc.qc.breakpoints, palmwtc.qc.ml, palmwtc.flux.scaling, and palmwtc.validation.science.