The MEMC model configuration for BAMS
BAMS_model.RdThe BAMS configuration is based off of Tang et al. 2022, this model uses MM for the DOM uptake, MM for POM decomposition, and a LM for MB decay, see dynamics for more details.
Format
an object created form configure_model, containing the following elements.
- name
BAMS
- table
table of the dynamics used by this model configuration, see dynamics for more details.
- params
data table of the model parameters, see default_params for more details.
- state
vector of the initial state values, see default_initial for more details.
See also
Other configurations:
COMISSION_model,
CORPSE_model,
MEMS_model,
MEND_model,
MIMCS_model,
model_configs
Examples
## Use solve_model to run the simulation using this configuration.
print(BAMS_model)
#> $name
#> [1] "BAMS"
#>
#> $table
#> model DOMuptake POMdecomp MBdecay
#> 1 BAMS MM MM LM
#>
#> $params
#> parameter description
#> 1 V_p maximum specific decomposition rate for POM by EP
#> 2 K_p half-saturation constant for decomposition of POM
#> 3 V_m maximum specific decomposition rate for MOM by EM
#> 4 K_m half-saturation constant for decomposition of MOM
#> 5 V_d maximum specific uptake rate of D for growth of MB
#> 6 K_d half-saturation constant of uptake of D for growth of MB
#> 7 f_d fraction of decomposed P allocated to DOM
#> 8 g_d fraction of dead B allocated to DOM
#> 9 p_ep fraction of mR for production of EP
#> 10 p_em fraction of mR for production of EM
#> 11 r_ep turnover rate of EP
#> 12 r_em turnover rate of EM
#> 13 Q_max maximum DOC sorption capacity
#> 14 K_ads specific adsorption rate
#> 15 K_des desorption rate
#> 16 dd_beta strength of density dependent microbial decay
#> 17 Input_POM POM input
#> 18 Input_DOM DOM input
#> 19 Input_MOM MOM input
#> 20 CUE carbon use efficiency
#> units value
#> 1 mgC mgC^-1 h^-1 14.000
#> 2 mgC / g soil 50.000
#> 3 mgC mgC^-1 h^-1 0.250
#> 4 mg C/g soil 250.000
#> 5 mgC mgC^-1 h^-1 3.000
#> 6 mg C/g soil 0.250
#> 7 <NA> 0.500
#> 8 <NA> 0.500
#> 9 <NA> 0.010
#> 10 <NA> 0.010
#> 11 mgC mgC^-1 h^-1 0.001
#> 12 mgC mgC^-1 h^-1 0.001
#> 13 mgC / g soil 3.400
#> 14 mgC mgC^-1 h^-1 0.006
#> 15 mgC mgC^-1 h^-1 0.001
#> 16 <NA> 1.000
#> 17 mg C 0.000
#> 18 mg C 0.000
#> 19 mg C 0.000
#> 20 0.400
#>
#> $state
#> POM MOM QOM MB DOM EP EM IC
#> 10.00000 5.00000 0.10000 2.00000 1.00000 0.00001 0.00001 0.00000
#> Tot
#> 18.10002
#>
solve_model(mod = MEMS_model, time = 1:10)
#> time variable value units name
#> 1: 1 POM 1.000000e+01 mg C/g soil MEMS
#> 2: 2 POM 8.818304e-02 mg C/g soil MEMS
#> 3: 3 POM 4.485527e-02 mg C/g soil MEMS
#> 4: 4 POM 2.175292e-02 mg C/g soil MEMS
#> 5: 5 POM 1.052347e-02 mg C/g soil MEMS
#> 6: 6 POM 5.094580e-03 mg C/g soil MEMS
#> 7: 7 POM 2.470695e-03 mg C/g soil MEMS
#> 8: 8 POM 1.202598e-03 mg C/g soil MEMS
#> 9: 9 POM 5.904516e-04 mg C/g soil MEMS
#> 10: 10 POM 2.932550e-04 mg C/g soil MEMS
#> 11: 1 MOM 5.000000e+00 mg C/g soil MEMS
#> 12: 2 MOM 1.063741e+01 mg C/g soil MEMS
#> 13: 3 MOM 1.109063e+01 mg C/g soil MEMS
#> 14: 4 MOM 1.131369e+01 mg C/g soil MEMS
#> 15: 5 MOM 1.142133e+01 mg C/g soil MEMS
#> 16: 6 MOM 1.147306e+01 mg C/g soil MEMS
#> 17: 7 MOM 1.149777e+01 mg C/g soil MEMS
#> 18: 8 MOM 1.150942e+01 mg C/g soil MEMS
#> 19: 9 MOM 1.151476e+01 mg C/g soil MEMS
#> 20: 10 MOM 1.151705e+01 mg C/g soil MEMS
#> 21: 1 QOM 1.000000e-01 mg C/g soil MEMS
#> 22: 2 QOM 1.135088e-01 mg C/g soil MEMS
#> 23: 3 QOM 1.171584e-01 mg C/g soil MEMS
#> 24: 4 QOM 1.187808e-01 mg C/g soil MEMS
#> 25: 5 QOM 1.195438e-01 mg C/g soil MEMS
#> 26: 6 QOM 1.198953e-01 mg C/g soil MEMS
#> 27: 7 QOM 1.200481e-01 mg C/g soil MEMS
#> 28: 8 QOM 1.201049e-01 mg C/g soil MEMS
#> 29: 9 QOM 1.201152e-01 mg C/g soil MEMS
#> 30: 10 QOM 1.201032e-01 mg C/g soil MEMS
#> 31: 1 MB 2.000000e+00 mg C/g soil MEMS
#> 32: 2 MB 2.013714e+00 mg C/g soil MEMS
#> 33: 3 MB 1.013229e+00 mg C/g soil MEMS
#> 34: 4 MB 4.910671e-01 mg C/g soil MEMS
#> 35: 5 MB 2.375647e-01 mg C/g soil MEMS
#> 36: 6 MB 1.150177e-01 mg C/g soil MEMS
#> 37: 7 MB 5.579123e-02 mg C/g soil MEMS
#> 38: 8 MB 2.716780e-02 mg C/g soil MEMS
#> 39: 9 MB 1.333500e-02 mg C/g soil MEMS
#> 40: 10 MB 6.649165e-03 mg C/g soil MEMS
#> 41: 1 DOM 1.000000e+00 mg C/g soil MEMS
#> 42: 2 DOM 9.976932e-01 mg C/g soil MEMS
#> 43: 3 DOM 4.055658e-01 mg C/g soil MEMS
#> 44: 4 DOM 1.939209e-01 mg C/g soil MEMS
#> 45: 5 DOM 9.385554e-02 mg C/g soil MEMS
#> 46: 6 DOM 4.556182e-02 mg C/g soil MEMS
#> 47: 7 DOM 2.222404e-02 mg C/g soil MEMS
#> 48: 8 DOM 1.094514e-02 mg C/g soil MEMS
#> 49: 9 DOM 5.493829e-03 mg C/g soil MEMS
#> 50: 10 DOM 2.859810e-03 mg C/g soil MEMS
#> 51: 1 EP 1.000000e-05 mg C/g soil MEMS
#> 52: 2 EP 2.781807e-02 mg C/g soil MEMS
#> 53: 3 EP 4.541118e-02 mg C/g soil MEMS
#> 54: 4 EP 5.401600e-02 mg C/g soil MEMS
#> 55: 5 EP 5.814889e-02 mg C/g soil MEMS
#> 56: 6 EP 6.011679e-02 mg C/g soil MEMS
#> 57: 7 EP 6.103831e-02 mg C/g soil MEMS
#> 58: 8 EP 6.145415e-02 mg C/g soil MEMS
#> 59: 9 EP 6.162562e-02 mg C/g soil MEMS
#> 60: 10 EP 6.167904e-02 mg C/g soil MEMS
#> 61: 1 EM 1.000000e-05 mg C/g soil MEMS
#> 62: 2 EM 2.781807e-02 mg C/g soil MEMS
#> 63: 3 EM 4.541118e-02 mg C/g soil MEMS
#> 64: 4 EM 5.401600e-02 mg C/g soil MEMS
#> 65: 5 EM 5.814889e-02 mg C/g soil MEMS
#> 66: 6 EM 6.011679e-02 mg C/g soil MEMS
#> 67: 7 EM 6.103831e-02 mg C/g soil MEMS
#> 68: 8 EM 6.145415e-02 mg C/g soil MEMS
#> 69: 9 EM 6.162562e-02 mg C/g soil MEMS
#> 70: 10 EM 6.167904e-02 mg C/g soil MEMS
#> 71: 1 IC 0.000000e+00 mg C/g soil MEMS
#> 72: 2 IC 4.193876e+00 mg C/g soil MEMS
#> 73: 3 IC 5.337757e+00 mg C/g soil MEMS
#> 74: 4 IC 5.852773e+00 mg C/g soil MEMS
#> 75: 5 IC 6.100903e+00 mg C/g soil MEMS
#> 76: 6 IC 6.221155e+00 mg C/g soil MEMS
#> 77: 7 IC 6.279638e+00 mg C/g soil MEMS
#> 78: 8 IC 6.308271e+00 mg C/g soil MEMS
#> 79: 9 IC 6.322476e+00 mg C/g soil MEMS
#> 80: 10 IC 6.329709e+00 mg C/g soil MEMS
#> 81: 1 Tot 1.810002e+01 mg C/g soil MEMS
#> 82: 2 Tot 1.390614e+01 mg C/g soil MEMS
#> 83: 3 Tot 1.276226e+01 mg C/g soil MEMS
#> 84: 4 Tot 1.224725e+01 mg C/g soil MEMS
#> 85: 5 Tot 1.199912e+01 mg C/g soil MEMS
#> 86: 6 Tot 1.187887e+01 mg C/g soil MEMS
#> 87: 7 Tot 1.182038e+01 mg C/g soil MEMS
#> 88: 8 Tot 1.179175e+01 mg C/g soil MEMS
#> 89: 9 Tot 1.177754e+01 mg C/g soil MEMS
#> 90: 10 Tot 1.177031e+01 mg C/g soil MEMS
#> time variable value units name