Change Model Parameters

This example will show how to update the model parameter values for any MEMC model configuration.

# Assumes MEMC has already been installed. 
library(MEMC) 

The MEMC package includes default parameter and initial pool values that are included as package data that are based on Wang et al. 2015¹. This example will use these values and show users how to update these values. We will also be running the MEMC MEND model configuration.

Default Parameters

Start by taking a look at the default model parameter values.

print(memc_initial_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
# Alternatively can use the :: to access the MEMC package data. 
# print(MEMC::memc_initial_state)

print(memc_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
# Alternatively can use the :: to access the MEMC package data. 
# print(MEMC::memc_params)

Run deafult MEMC MEND

Run the pre-configured MEMC MEND model with the default parameter values.

time <- 0:600 
mod1 <- MEND_config
out1 <- memc_solve(mod = mod1, time = time)
out1$name <- "Km = 250 (default)"

Update parameter value

Users can update the parameters directly via memc_solve. Any parameter(s) value(s) fed into the memc_solve params argument will overwrite the parameter values defined the model configuration.

out2 <- memc_solve(mod = MEND_config, time = time, params = c("K_m" = 10))
out2$name <- "Km = 10 (lower)"

ggplot(data = rbind(out1, out2)) + 
  geom_line(aes(time, value, color = name, linetype = name), linewidth = 0.75) + 
  facet_wrap("variable", scales = "free") + 
  labs(y = "mg C/g soil", 
       title = "Change Km Values") +
  theme(legend.title = element_blank())

Update parameter table using memc_update_params

memc_update_params is a helper function that can change the parameter values in the parameter table. You will need to set up a new model configuration with the new parameter table.

new_km <- memc_update_params(new_params = c("K_m" = 100), param_table = memc_params)

# Set up the new model configuration with the 
mod_km <- memc_configure(params = new_km, 
                        state = memc_initial_state,
                        name = "Km = 100", 
                        DOMuptake = "MM",
                        POMdecomp = "MM",
                        MBdecay = "LM")

out3 <- memc_solve(mod = mod_km, time = time)

ggplot(data = rbind(out1, out2, out3)) + 
  geom_line(aes(time, value, color = name, linetype = name), linewidth = 0.75) + 
  facet_wrap("variable", scales = "free") + 
  labs(y = "mg C/g soil", 
       title = "Change Km Values") +
  theme(legend.title = element_blank())