new scripts to run the metabolism model incl diffusion

Author: robertladwig

src/odem_min_indexed_sed.stan

@@ -143,7 +143,7 @@ transformed parameters {
         mineral[i] = MIN[i_Param[i]] * theta0[i-1];
 	      //sed2[i] = SED2[i_Param[i]] *  (fmax((DO_tot[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_tot[i-1]*tau+mu),1e-06))) * theta0[i-1] / mean_depth + DO_tot[i-1] * diff_mol/z_dbl * theta0[i-1] / mean_depth;
         sed_monod[i] = (SED2[i_Param[i]] *  theta0[i-1] )/ mean_depth; //fmax(fmax((DO_tot[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_tot[i-1]*tau+mu),1e-06)),1e-06) *
-        // fmax((DO_tot[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_tot[i-1]*tau+mu),1e-06))
+        // fmax((DO_tot[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_tot[i-1]*tau+mu),1e-06)) 
         // sed_first[i] = fmax(fmax((DO_tot[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_tot[i-1]*tau+mu),1e-06)),1e-06) * (fmax((DO_tot[i-1]*tau + mu),1e-06) * diff_mol/z_dbl * theta0[i-1]) / fmax((volume_tot[i-1]/area_epi[i-1]),1);
         sed_first[i] = ((fmax((DO_tot[i-1]*tau + mu),1e-06) * diff_mol[i-1]/(z_dbl * max_depth) * theta0[i-1]))/tau;
         sed2[i] = sed_monod[i] +  sed_first[i];
@@ -183,7 +183,7 @@ transformed parameters {
     	 mineral[i] = MIN[i_Param[i]] * theta2[i-1];
 	     //sed2[i] = (SED2[i_Param[i]] *  (fmax((DO_hyp[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_hyp[i-1]*tau+mu),1e-06))) * theta2[i-1]) / fmax((volume_hyp[i-1]/area_hyp[i-1]),1) + (DO_hyp[i-1] * diff_mol/z_dbl* theta2[i-1]) / fmax((volume_hyp[i-1]/area_hyp[i-1]),1);
        sed_monod[i] = (SED2[i_Param[i]] *  theta2[i-1]) / fmax((volume_hyp[i-1]/area_hyp[i-1]),1);// fmax(fmax((DO_hyp[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_hyp[i-1]*tau+mu),1e-06)),1e-06) *
-       // fmax((DO_hyp[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_hyp[i-1]*tau+mu),1e-06))
+       // fmax((DO_hyp[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_hyp[i-1]*tau+mu),1e-06)) 
        // sed_first[i] =fmax(fmax((DO_hyp[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_hyp[i-1]*tau+mu),1e-06)),1e-06) *  (fmax((DO_hyp[i-1]*tau + mu),1e-06) * diff_mol/z_dbl* theta2[i-1]) / fmax((volume_hyp[i-1]/area_hyp[i-1]),1);
        sed_first[i] =  ((fmax((DO_hyp[i-1]*tau + mu),1e-06) * diff_mol[i-1]/(fmax((volume_hyp[i-1]/area_hyp[i-1]),1)*z_dbl) * theta2[i-1]) ) /tau;
        sed2[i] = sed_monod[i] +  sed_first[i];

src/odem_min_indexed_sed_south.stan

@@ -143,7 +143,7 @@ transformed parameters {
         mineral[i] = MIN[i_Param[i]] * theta0[i-1];
 	      //sed2[i] = SED2[i_Param[i]] *  (fmax((DO_tot[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_tot[i-1]*tau+mu),1e-06))) * theta0[i-1] / mean_depth + DO_tot[i-1] * diff_mol/z_dbl * theta0[i-1] / mean_depth;
         sed_monod[i] = (SED2[i_Param[i]] *  theta0[i-1] )/ mean_depth; //fmax(fmax((DO_tot[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_tot[i-1]*tau+mu),1e-06)),1e-06) *
-        // fmax((DO_tot[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_tot[i-1]*tau+mu),1e-06)) 
+        // fmax((DO_tot[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_tot[i-1]*tau+mu),1e-06))
         // sed_first[i] = fmax(fmax((DO_tot[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_tot[i-1]*tau+mu),1e-06)),1e-06) * (fmax((DO_tot[i-1]*tau + mu),1e-06) * diff_mol/z_dbl * theta0[i-1]) / fmax((volume_tot[i-1]/area_epi[i-1]),1);
         sed_first[i] = ((fmax((DO_tot[i-1]*tau + mu),1e-06) * diff_mol[i-1]/(z_dbl * max_depth) * theta0[i-1]))/tau;
         sed2[i] = sed_monod[i] +  sed_first[i];
@@ -183,7 +183,7 @@ transformed parameters {
     	 mineral[i] = MIN[i_Param[i]] * theta2[i-1];
 	     //sed2[i] = (SED2[i_Param[i]] *  (fmax((DO_hyp[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_hyp[i-1]*tau+mu),1e-06))) * theta2[i-1]) / fmax((volume_hyp[i-1]/area_hyp[i-1]),1) + (DO_hyp[i-1] * diff_mol/z_dbl* theta2[i-1]) / fmax((volume_hyp[i-1]/area_hyp[i-1]),1);
        sed_monod[i] = (SED2[i_Param[i]] *  theta2[i-1]) / fmax((volume_hyp[i-1]/area_hyp[i-1]),1);// fmax(fmax((DO_hyp[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_hyp[i-1]*tau+mu),1e-06)),1e-06) *
-       // fmax((DO_hyp[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_hyp[i-1]*tau+mu),1e-06)) 
+       // fmax((DO_hyp[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_hyp[i-1]*tau+mu),1e-06))
        // sed_first[i] =fmax(fmax((DO_hyp[i-1]*tau+mu),1e-06)/(khalf + fmax((DO_hyp[i-1]*tau+mu),1e-06)),1e-06) *  (fmax((DO_hyp[i-1]*tau + mu),1e-06) * diff_mol/z_dbl* theta2[i-1]) / fmax((volume_hyp[i-1]/area_hyp[i-1]),1);
        sed_first[i] =  ((fmax((DO_hyp[i-1]*tau + mu),1e-06) * diff_mol[i-1]/(fmax((volume_hyp[i-1]/area_hyp[i-1]),1)*z_dbl) * theta2[i-1]) ) /tau;
        sed2[i] = sed_monod[i] +  sed_first[i];

src/run_odem_chtc_sed.R

@@ -106,7 +106,7 @@ for (i in 2:nParamEstimates){
 }
 
 
-buoy.freq <- sqrt((get_dens(in1yr$temperature_hypo,0) - get_dens(in1yr$temperature_epi,0))/(in1yr$lower_meta - in1yr$upper_meta)* 9.81/998.2)
+buoy.freq <- ((get_dens(in1yr$temperature_hypo,0) - get_dens(in1yr$temperature_epi,0))/(in1yr$lower_meta - in1yr$upper_meta)* 9.81/998.2)
 buoy.freq[which(buoy.freq<7e-5)] = 7e-5
 kz = 0.00706 * (mean(in1yr$area_surface))^(0.56) * buoy.freq^(-0.43)
 kz[which(is.na(kz))] = 1e-10

src/run_odem_chtc_sed_south.R

@@ -106,7 +106,7 @@ for (i in 2:nParamEstimates){
 }
 
 
-buoy.freq <- sqrt((get_dens(in1yr$temperature_hypo,0) - get_dens(in1yr$temperature_epi,0))/(in1yr$lower_meta - in1yr$upper_meta)* 9.81/998.2)
+buoy.freq <- ((get_dens(in1yr$temperature_hypo,0) - get_dens(in1yr$temperature_epi,0))/(in1yr$lower_meta - in1yr$upper_meta)* 9.81/998.2)
 buoy.freq[which(buoy.freq<7e-5)] = 7e-5
 kz = 0.00706 * (mean(in1yr$area_surface))^(0.56) * buoy.freq^(-0.43)
 kz[which(is.na(kz))] = 1e-10