In ashiklom/fortebaseline: Forest Resilience and Threshold Experiment (FoRTE) ED2 baseline runs source code and manuscript

Three parameters are related to leaf-level physiology: Following the enzyme-kinetic model of @farquhar_1980_biochemical, the rate of photosynthesis is the minimum of light-limited and enzyme-limited reactions. The former are controlled by the quantum efficiency parameter---maximum efficiency with which absorbed photosynthetically active radiation is converted to CO~2~. The latter are controlled by V~cmax~, the maximum rate of carbon fixation by Rubisco. The water demand of photosynthesis is controlled by the stomatal slope, the sensitivity of stomatal conductance of CO~2~ as a function of CO~2~ concentration and humidity at the leaf surface [@leuning_1995_critical; @ball_1987_model]. Three more parameters correspond to the respiration rates of leaves, roots, and "growth maintenance".

Two more parameters control carbon allocation: One is the ratio of fine root to leaf biomass (fineroot2leaf, or q), and another is the ratio of "storage" carbon allocated to reproduction (r_fract).

Three parameters control various aspects of adult tree mortality. The overall adult mortality rate in ED-2.2 ($M$) is the sum of density-independent mortality from aging ($M_I$, plants year^-1^), density-dependent mortality from C starvation ($M_D$), and mortality from cold/frost ($M_F$) (ED-2.2 technically also includes additional term for fire mortality, but we did not include fire in our simulations):

$$ M = M_I + M_D + M_F $$

Density-independent mortality from aging ($M_I$) is a prescribed, PFT-specific parameter (mort3). Density-dependent mortality from C starvation is calculated as a function of a cohort's C balance limitation:

$$ M_D = \frac{y_1}{1 + \exp\left[y_2 \left( \frac{C_k}{C_k^*} \right)\right]} $$

where $C_k$ is the 12 month running mean C balance of the cohort, $C_k^*$ is the running mean ideal C balance if there was no light or water limitation, and $y_1$ (mort1; plants year^-1^) and $y_2$ (mort2; unitless) are PFT-specific parameters. Seedling mortality rate is prescribed as its own PFT-specific parameter.

Several parameters are related to canopy structure and radiative transfer. Specific leaf area (SLA) is used to convert leaf biomass to leaf area index, which in turn is used in a variety of calculations related to canopy radiative transfer and micrometeorology. Canopy clumping factor describes how evenly leaf area is distributed in horizontal space (1 being perfectly evenly; 0 being a "black hole" where all leaves are concentrated in a single point); and leaf orientation factor describes the average distribution of leaf angles (-1 being perfectly vertical, 1 being perfectly horizontal, and 0 being random). Four parameters control leaf optical properties, namely the fractions of light reflected or transmitted in visible and near-infrared wavelengths (leaf_(reflect|trans)_(vis|nir)). Details of how these parameters influence canopy radiative transfer are described in the Supplementary Information.

Other parameters (TODO, briefly):

• Fraction of litter carbon that enters the labile (fast) soil carbon pool (f_labile)
• Minimum plant height for reproduction (repro_min_h)
• Soil-plant water conductance, or "water availability factor" (water_conductance)
• C:N ratio in fine roots (c2n_fineroot) and leaves (c2n_leaf)
• Leaf turnover rate (evergreen-only; leaf_turnover_rate)
• Proportion of dispersal that is "global" (nonlocal_dispersal)

ashiklom/fortebaseline documentation built on May 9, 2020, 1:56 a.m.