Corrections and clarifications to heterotrophic respiration scheme

[dlebauer]

Description

Based on conversation today, this equation was incorrect because the $f_\text{litter}$ only applies to litter, not to soil (since decomposed soil is either respired or stays in the soil pool).

In addition to clarifying and fixing heterotrophic respiration, I also clarified the section and fixed typos and other inconsistencies.

This was incorrect

Correct (🤞🏻):

---

Side note on notation

Currently, fluxes are (hopefully consistently) indexed by their destination pool, but this is ambiguous e.g.:

$$\large{F^C_\text{soil}}$$

is the flux to soil, but could refer to flux from roots, litter, or OM additions. I've changed some of these to use

$$\large{F_\text{to, from}}$$

notation but perhaps it would be more clear to make it

$$\large{F_{\text{from}\rightarrow \text{to}}}$$

If so I can write this up as perhaps a 'good first issue' to follow #203.

[Copilot]

Pull request overview

This PR corrects the heterotrophic respiration equations in the model documentation by properly separating litter and soil respiration components. The key fix addresses an error where the respiration fraction parameter $f_{\text{litter}}$ was incorrectly applied to both litter and soil pools, when it should only apply to litter decomposition.

Key Changes:

• Reformulated the heterotrophic respiration equation to explicitly separate soil and litter respiration components
• Clarified that litter decomposition is partitioned between respiration and soil carbon transfer using $f_{\text{litter}}$
• Updated parameter tables to improve notation consistency and remove deprecated/unused parameters
• Cleaned up documentation by removing commented-out sections and consolidating parameter descriptions

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 7 comments.

File	Description
docs/parameters.md	Renamed "Litter Quality Parameters" to "Stoichiometry Parameters", updated parameter symbols (including $f_{\text{litter}}$ and CN parameters), added methane oxidation rate parameter, removed deprecated microbe and methane parameter sections, and cleaned up formatting
docs/model-structure.md	Restructured heterotrophic respiration section to separate litter and soil components, added new equations (4a, 4b) to clarify litter decomposition partitioning, rewrote explanatory text for improved clarity, and removed the old combined respiration equation that incorrectly applied $f_{R_H}$ to both pools

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 2 out of 2 changed files in this pull request and generated 4 comments.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Alomir]

A couple of minor comments:

1. In Eq 3 in the screenshot above, I don't think the "fert" in the LHS is relevant; the RHS is more than just the fert contribution.
2. I like the F_{from->to} form, hard to misinterpret that. OK, harder to misinterpret that...

[Alomir]

Another comment - so we are concluding that litter decomp/respiration does NOT need the CN or tillage dependency term?

Hmmm, hold on, mis-read...

Don't the two R_H_litter calcs - (5) and last part of (7) - contradict each other?

[Alomir]

One more - I think harvest plays in to dC_soil/dt (eq Braswell A3), unless we are implicitly including it in the belowground plant turnover.

[Alomir]

This is redundant with the paragraph above, yes?

[dlebauer]

good point. Fixed in 16bd4be

[dlebauer]

Suggested change

	$F^C_{\text{decomp}}$ is the total litter decomposition flux, representing the rate at which litter carbon is processed by microbial activity.
	$F^C_{\text{decomp}}$ is the total litter decomposition flux, representing the rate at which litter carbon is processed by microbial activity prior to partitioning among downstream fluxes.