remove the Input MOM

Microbial-Explicit-Model · Aug 31, 2023 · 05259ce · 05259ce
1 parent 31fe0bf
commit 05259ce
Show file tree

Hide file tree

Showing 18 changed files with 28 additions and 31 deletions.
diff --git a/R/model_componet.R b/R/model_componet.R
@@ -130,7 +130,7 @@ carbon_pool_derivs <-
       # POM = particulate organic carbon
       dPOM <- (1 - p[["g_d"]]) * F6 - F2 + p[["Input_POM"]]
       # MOM = mineral-associated organic carbon (MOC)
-      dMOM <- (1 - p[["f_d"]]) * F2 - F3 + p[["Input_MOM"]]
+      dMOM <- (1 - p[["f_d"]]) * F2 - F3 
       # QOMO = active layer of MOC
       dQOM <- F4 - F5
       # MB = microbial biomass carbon
@@ -145,7 +145,7 @@ carbon_pool_derivs <-
       # IC = inorganic carbon (CO2)
       dIC <- F1 * (1 - p[["CUE"]])
       # Tot = the total carbon pool
-      dTot <- -F1 * (1 - p[["CUE"]]) +  (p[["Input_POM"]] + p[["Input_DOM"]] + p[["Input_MOM"]])
+      dTot <- -F1 * (1 - p[["CUE"]]) +  (p[["Input_POM"]] + p[["Input_DOM"]])
 
       # Return outputs
       return(list(c(dPOM, dMOM, dQOM, dMB, dDOM, dEP, dEM, dIC, dTot)))

diff --git a/README.md b/README.md
@@ -94,8 +94,7 @@ print(MEND_model)
 #> 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
+#> 19       CUE                                    carbon use efficiency
 #>              units   value
 #> 1  mgC mgC^-1 h^-1  14.000
 #> 2     mgC / g soil  50.000
@@ -115,8 +114,7 @@ print(MEND_model)
 #> 16            <NA>   1.000
 #> 17            mg C   0.000
 #> 18            mg C   0.000
-#> 19            mg C   0.000
-#> 20                   0.400
+#> 19                   0.400
 #> 
 #> $state
 #>      POM      MOM      QOM       MB      DOM       EP       EM       IC 

diff --git a/data-raw/default_params.csv b/data-raw/default_params.csv
@@ -1,21 +1,20 @@
-parameter,description,units,value
-V_p,maximum specific decomposition rate for POM by EP,mgC mgC^-1 h^-1,14
-K_p,half-saturation constant for decomposition of POM,mgC / g soil,50
-V_m,maximum specific decomposition rate for MOM by EM,mgC mgC^-1 h^-1,0.25
-K_m,half-saturation constant for decomposition of MOM,mg C/g soil,250
-V_d,maximum specific uptake rate of D for growth of MB,mgC mgC^-1 h^-1,3.00E+00
-K_d,half-saturation constant of uptake of D for growth of MB,mg C/g soil,0.25
-f_d,fraction of decomposed P allocated to DOM,NA,0.5
-g_d,fraction of dead B allocated to DOM,NA,0.5
-p_ep,fraction of mR for production of EP,NA,0.01
-p_em,fraction of mR for production of EM,NA,0.01
-r_ep,turnover rate of EP,mgC mgC^-1 h^-1,0.001
-r_em,turnover rate of EM,mgC mgC^-1 h^-1,0.001
-Q_max,maximum DOC sorption capacity,mgC / g soil,3.4
-K_ads,specific adsorption rate,mgC mgC^-1 h^-1,0.006
-K_des,desorption rate,mgC mgC^-1 h^-1,0.001
-dd_beta,strength of density dependent microbial decay,NA,1
-Input_POM,POM input ,mg C,0
-Input_DOM,DOM input,mg C,0
-Input_MOM,MOM input ,mg C,0
+parameter,description,units,value
+V_p,maximum specific decomposition rate for POM by EP,mgC mgC^-1 h^-1,14
+K_p,half-saturation constant for decomposition of POM,mgC / g soil,50
+V_m,maximum specific decomposition rate for MOM by EM,mgC mgC^-1 h^-1,0.25
+K_m,half-saturation constant for decomposition of MOM,mg C/g soil,250
+V_d,maximum specific uptake rate of D for growth of MB,mgC mgC^-1 h^-1,3.00E+00
+K_d,half-saturation constant of uptake of D for growth of MB,mg C/g soil,0.25
+f_d,fraction of decomposed P allocated to DOM,NA,0.5
+g_d,fraction of dead B allocated to DOM,NA,0.5
+p_ep,fraction of mR for production of EP,NA,0.01
+p_em,fraction of mR for production of EM,NA,0.01
+r_ep,turnover rate of EP,mgC mgC^-1 h^-1,0.001
+r_em,turnover rate of EM,mgC mgC^-1 h^-1,0.001
+Q_max,maximum DOC sorption capacity,mgC / g soil,3.4
+K_ads,specific adsorption rate,mgC mgC^-1 h^-1,0.006
+K_des,desorption rate,mgC mgC^-1 h^-1,0.001
+dd_beta,strength of density dependent microbial decay,NA,1
+Input_POM,POM input ,mg C,0
+Input_DOM,DOM input,mg C,0
 CUE,carbon use efficiency,,0.4
diff --git a/data/BAMS_model.rda b/data/BAMS_model.rda
diff --git a/data/COMISSION_model.rda b/data/COMISSION_model.rda
diff --git a/data/CORPSE_model.rda b/data/CORPSE_model.rda
diff --git a/data/MEMS_model.rda b/data/MEMS_model.rda
diff --git a/data/MEND_model.rda b/data/MEND_model.rda
diff --git a/data/MIMCS_model.rda b/data/MIMCS_model.rda
diff --git a/data/default_initial.rda b/data/default_initial.rda
diff --git a/data/default_params.rda b/data/default_params.rda
diff --git a/data/model_configs.rda b/data/model_configs.rda
diff --git a/legacy/recreating_MEMC_Dec7.R b/legacy/recreating_MEMC_Dec7.R
@@ -15,7 +15,7 @@ desc <- c("maximum specific decomposition rate for P by EP", "half-saturation co
           "turnover rate of EP", "turnover rate of EM", "maximum DOC sorption capacity", "specific adsorption rate", "desorption rate", "strength of density dependent microbial decay",
           "POM input", "DOM input", "M input", "carbon use efficiency")
 value <- c("V_p"=14, "K_p"=50, "V_m"=0.25, "K_m"=250, "V_d"=3, "K_d"=0.25, "f_d"=0.5, "g_d"=0.5, "p_ep"=0.01, "p_em"=0.01, "r_ep"=1e-3, "r_em"=1e-3 , "Q_max"=3.4, "K_ads"=0.006,
-           "K_des"= 0.001, "dd_beta" = 2, "Input_POM" = 0, "Input_DOM"=0, "Input_MOM"=0, "CUE"=0.4)
+           "K_des"= 0.001, "dd_beta" = 2, "Input_POM" = 0, "Input_DOM"=0, "CUE"=0.4)
 units <- c("mgC mgC^-1 h^-1", "mgC / g soil", "mgC mgC^-1 h^-1", "mg C/g soil", "mgC mgC^-1 h^-1", "mg C/g soil", NA,
            NA, NA, NA, "mgC mgC^-1 h^-1", "mgC mgC^-1 h^-1", "mgC / g soil", "mgC mgC^-1 h^-1", "mgC mgC^-1 h^-1", NA,
            "mg C", "mg C", "mg C", "")

diff --git a/man/figures/README-unnamed-chunk-6-1.png b/man/figures/README-unnamed-chunk-6-1.png
diff --git a/man/figures/README-unnamed-chunk-9-1.png b/man/figures/README-unnamed-chunk-9-1.png
diff --git a/tests/testthat/test-argument.R b/tests/testthat/test-argument.R
@@ -10,7 +10,7 @@ test_that("is_param_table works", {
   # A number of errors should be thrown if the the parameter table does not meet the correct conditions.
   expect_error(
     is_param_table(params[1:10, ]),
-    "param_table is missing a parameter value(s) for: r_ep, r_em, Q_max, K_ads, K_des, dd_beta, Input_POM, Input_DOM, Input_MOM, CUE",
+    "param_table is missing a parameter value(s) for: r_ep, r_em, Q_max, K_ads, K_des, dd_beta, Input_POM, Input_DOM, CUE",
     fixed = TRUE
   )
 

diff --git a/tests/testthat/test-helper.R b/tests/testthat/test-helper.R
@@ -54,7 +54,7 @@ test_that("bad model configuration will fail", {
   # Errors should be thrown
   expect_error(
     configure_model(ptable[1:9,], state),
-   "param_table is missing a parameter value(s) for: p_em, r_ep, r_em, Q_max, K_ads, K_des, dd_beta, Input_POM, Input_DOM, Input_MOM, CUE",
+   "param_table is missing a parameter value(s) for: p_em, r_ep, r_em, Q_max, K_ads, K_des, dd_beta, Input_POM, Input_DOM, CUE",
     fixed = TRUE
   )
   expect_error(

diff --git a/tests/testthat/test-jz.R b/tests/testthat/test-jz.R
@@ -12,7 +12,7 @@
 #
 # params <- c("V_p", "K_p", "V_m", "K_m", "V_d", "K_d", "f_d", "g_d", "p_ep",
 #             "p_em", "r_ep", "r_em", "Q_max", "K_ads",
-#             "K_des", "dd_beta", "Input_POM", "Input_DOM", "Input_MOM", "CUE")
+#             "K_des", "dd_beta", "Input_POM", "Input_DOM", "CUE")
 # desc <- c("maximum specific decomposition rate for P by EP", "half-saturation constant for decomposition of P",
 #           "maximum specific decomposition rate for M by EM",
 #           "half-saturation constant for decomposition of M",
@@ -26,7 +26,7 @@
 # value <- c("V_p" = 14, "K_p" = 50, "V_m" = 0.25, "K_m" = 250, "V_d" = 3, "K_d"= 0.25,
 #            "f_d" = 0.5, "g_d" = 0.5, "p_ep" = 0.01, "p_em" = 0.01, "r_ep" = 1e-3,
 #            "r_em" = 1e-3 , "Q_max" = 3.4, "K_ads" = 0.006, "K_des"= 0.001, "dd_beta" = 2,
-#            "Input_POM" = 0, "Input_DOM" = 0, "Input_MOM" = 0, "CUE" = 0.4)
+#            "Input_POM" = 0, "Input_DOM" = 0, "CUE" = 0.4)
 # units <- c("mgC mgC^-1 h^-1", "mgC / g soil", "mgC mgC^-1 h^-1", "mg C/g soil",
 #            "mgC mgC^-1 h^-1", "mg C/g soil", NA,
 #            NA, NA, NA, "mgC mgC^-1 h^-1", "mgC mgC^-1 h^-1", "mgC / g soil",