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Hi Ayn,
You are correct that the ST-Sim stock flow add-on can be used to track snags and downed wood. Stock flow models typically maintain a mass balance across all stocks so it is best to include stocks for live biomass, atmosphere and soil also. A really good example that includes snags and downed wood is included as a template from the ST-Sim CBM-CFS3 add-on package which includes flow pathways and rates from live to snag and snag to downed wood stocks. Typically the rates are both included for automatic flows (i.e., biomass turnover from natural mortality) and disturbance driven flows (i.e., wildfire and timber harvest).
Here is the landing page for the ST-Sim CBM-CFS3 add-on which includes a “Getting Started” guide: https://apexrms.github.io/stsimcbmcfs3/
A paper worth reading is Sleeter et al. 2022: https://doi.org/10.1186/s13021-022-00201-1
Hope this helps!
Regards,
Leonardo