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The MEMS configuration is based off of Robertson et al. 2019. This model uses LM for the DOM uptake, LM for POM decomposition, and LM for MB decay; see dynamics for more details.

Usage

MEMS_config

Format

An object created from memc_configure, containing the following elements.

name

MEMS

table

table of the dynamics used by this model configuration; see dynamics for more details.

params

data table of the model parameters; see memc_params for more details.

state

vector of the initial state values; see memc_initial_state for more details.

Examples

## Use memc_solve to run the simulation using this configuration.
print(MEMS_config)
#> $name
#> [1] "MEMS"
#> 
#> $table
#>   model DOMuptake POMdecomp MBdecay
#> 1  MEMS        LM        LM      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       CUE                                    carbon use efficiency
#>              units   value
#> 1  mgC mgC^-1 d^-1  14.000
#> 2     mgC / g soil  50.000
#> 3  mgC mgC^-1 d^-1   0.250
#> 4      mg C/g soil 250.000
#> 5  mgC mgC^-1 d^-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 d^-1   0.001
#> 12 mgC mgC^-1 d^-1   0.001
#> 13    mgC / g soil   3.400
#> 14 mgC mgC^-1 d^-1   0.006
#> 15 mgC mgC^-1 d^-1   0.001
#> 16            <NA>   1.000
#> 17            mg C   0.000
#> 18            mg C   0.000
#> 19                   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 
#> 
memc_solve(mod = MEMS_config, time = 1:10)
#>      time variable        value       units   name
#>     <num>   <fctr>        <num>      <char> <char>
#>  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