File name	Function
FitCost_BasalFitness Source code 1	Calculates the cost function for monocultures (i.e. the difference between the target mechanistic model dynamics and the dynamics obtained from the pairwise model)
FitCost_BFSatLV.m Source code 2	Calculates the cost function for communities (i.e. the difference between the target mechanistic model dynamics and the dynamics obtained from the saturable L-V pairwise model)
FitCost_BFSatLV_Dp.m Source code 3	Calculates the cost function for communities (i.e. the difference between the target mechanistic model dynamics and the dynamics obtained from the alternative pairwise model)
DynamicsMM_WM_MonocultureDpMM.m Source code 4	Returns growth dynamics for monocultures, based on the mechanistic model
DynamicsMMSS_WM_NetworkDpMM.m Source code 5	Returns growth dynamics for communities of multiple species, based on the mechanistic model
DynamicsWM_NetworkBFSatLV.m Source code 6	Returns growth dynamics for communities of multiple species, based on the saturable L-V pairwise model
DynamicsWM_NetworkBFSatLV_Dp.m Source code 7	Returns growth dynamics for communities of multiple species, based on the alternative pairwise model
DeriveBasalFitnessMM_WM_DpMM.m Source code 8	Estimates monoculture parameters of pairwise model (Step 1)
DeriveBFSatLVMMSS_WM_DpMM.m Source code 9	Estimates saturable L-V pairwise model interaction parameters (Step 2)
DeriveBFSatLVMMSS_WM_DpMM_Dp.m Source code 10	Estimates alternative pairwise model interaction parameters (Step 2)
DeriveBFSatLVMMSS_WM_DpMM_r21.m Source code 11	Estimates saturable L-V pairwise model interaction parameters (${\displaystyle r_{21}}$ and ${\displaystyle K_{21}}$) in cases where we know that S2 is only affected by S1, to accelerate optimization
DeriveBFSatLVMM_WM_DpMM_Dp_r21.m Source code 12	Estimates alternative pairwise model interaction parameter (${\displaystyle r_{21}}$) in cases where we know that S2 is only affected by S1 and that ${\displaystyle K_{S2C1}=K_{C1S2}}$ to accelerate optimization
DynamicsWM_NetworkBFLogLV_DI.m Source code 13	Returns growth dynamics for communities of two species competing for an environmental resource while engaging in an additional interaction, based on the logistic L-V pairwise model (Figure 6)
C2Sp2_ARCLi_NoSatDp_FitBFLogLV_DI.m Source code 14	Estimates logistic L-V pairwise model interaction parameters for communities of two species competing for an environmental resource while engaging in an additional interaction, and compares community dynamics from pairwise and mechanistic models (Figure 6)
Dynamics_WM_NetworkDpMM_ODE23.m Source code 15	Defines differential equations when using Matlab’s ODE23 solver to calculate community dynamics
Case_C1Sp2_CmnsDp_ODE23.m Source code 16	Example of using Matlab ODE23 solver for calculating community dynamics