Coefficient matrix for formation fractions, no sink and one pathway

1 files changed, 26 insertions, 22 deletions

diff --git a/R/mkinmod.R b/R/mkinmod.R
index 1ffd14d7..eb290719 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -67,12 +67,12 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
       FOMC = varname,

       DFOP = varname,

       HS = varname,

-      SFORB = paste(varname, c("free", "bound"), sep="_")

+      SFORB = paste(varname, c("free", "bound"), sep = "_")

     )

     map[[varname]] <- new_boxes

     names(map[[varname]]) <- rep(spec[[varname]]$type, length(new_boxes)) #}}}

     # Start a new differential equation for each new box {{{

-    new_diffs <- paste("d_", new_boxes, " =", sep="")

+    new_diffs <- paste("d_", new_boxes, " =", sep = "")

     names(new_diffs) <- new_boxes

     diffs <- c(diffs, new_diffs) #}}}

   } #}}}

@@ -89,14 +89,14 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
       if (use_of_ff == "min") { # Minimum use of formation fractions

         if(spec[[varname]]$sink) {

           # If sink is required, add first-order sink term

-          k_compound_sink <- paste("k", box_1, "sink", sep="_")

+          k_compound_sink <- paste("k", box_1, "sink", sep = "_")

           parms <- c(parms, k_compound_sink)

           decline_term <- paste(k_compound_sink, "*", box_1)

         } else { # otherwise no decline term needed here

           decline_term = "0" 

         }

       } else {

-        k_compound <- paste("k", box_1, sep="_")

+        k_compound <- paste("k", box_1, sep = "_")

         parms <- c(parms, k_compound)

         decline_term <- paste(k_compound, "*", box_1)

       }

@@ -121,8 +121,8 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
     if(spec[[varname]]$type == "SFORB") { # {{{ Add SFORB reversible binding terms

       box_2 = map[[varname]][[2]]

       if (use_of_ff == "min") { # Minimum use of formation fractions

-        k_free_bound <- paste("k", varname, "free", "bound", sep="_")

-        k_bound_free <- paste("k", varname, "bound", "free", sep="_")

+        k_free_bound <- paste("k", varname, "free", "bound", sep = "_")

+        k_bound_free <- paste("k", varname, "bound", "free", sep = "_")

         parms <- c(parms, k_free_bound, k_bound_free)

         reversible_binding_term_1 <- paste("-", k_free_bound, "*", box_1, "+",

           k_bound_free, "*", box_2)

@@ -133,8 +133,8 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
         # The problems were: Calculation of dissipation times did not work in this case

         # and the coefficient matrix is not generated correctly by the code present 

         # in this file in this case

-        f_free_bound <- paste("f", varname, "free", "bound", sep="_")

-        k_bound_free <- paste("k", varname, "bound", "free", sep="_")

+        f_free_bound <- paste("f", varname, "free", "bound", sep = "_")

+        k_bound_free <- paste("k", varname, "bound", "free", sep = "_")

         parms <- c(parms, f_free_bound, k_bound_free)

         reversible_binding_term_1 <- paste("+", k_bound_free, "*", box_2)

         reversible_binding_term_2 <- paste("+", f_free_bound, "*", k_compound, "*", box_1, "-",

@@ -157,10 +157,10 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
       for (target in to) {

         target_box <- switch(spec[[target]]$type,

           SFO = target,

-          SFORB = paste(target, "free", sep="_"))

+          SFORB = paste(target, "free", sep = "_"))

         if (use_of_ff == "min" && spec[[varname]]$type %in% c("SFO",

           "SFORB")) {

-          k_from_to <- paste("k", origin_box, target_box, sep="_")

+          k_from_to <- paste("k", origin_box, target_box, sep = "_")

           parms <- c(parms, k_from_to)

           diffs[[origin_box]] <- paste(diffs[[origin_box]], "-", 

             k_from_to, "*", origin_box)

@@ -172,7 +172,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
             diffs[[target_box]] <- paste(diffs[[target_box]], "+",

                                          decline_term)

           } else {

-            fraction_to_target = paste("f", origin_box, "to", target, sep="_")

+            fraction_to_target = paste("f", origin_box, "to", target, sep = "_")

             parms <- c(parms, fraction_to_target)

             diffs[[target_box]] <- paste(diffs[[target_box]], "+", 

                 fraction_to_target, "*", decline_term)

@@ -194,7 +194,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
       for (from in boxes) {

         for (to in boxes) {

           if (from == to) { # diagonal elements

-            k.candidate = paste("k", from, c(boxes, "sink"), sep="_")

+            k.candidate = paste("k", from, c(boxes, "sink"), sep = "_")

             k.candidate = sub("free.*bound", "free_bound", k.candidate)

             k.candidate = sub("bound.*free", "bound_free", k.candidate)

             k.effective = intersect(model$parms, k.candidate)

@@ -202,12 +202,12 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
                 paste("-", k.effective, collapse = " "), "0")

 

           } else {          # off-diagonal elements

-            k.candidate = paste("k", from, to, sep="_")

+            k.candidate = paste("k", from, to, sep = "_")

 	    if (sub("_free$", "", from) == sub("_bound$", "", to)) {

-              k.candidate = paste("k", sub("_free$", "_free_bound", from), sep="_")

+              k.candidate = paste("k", sub("_free$", "_free_bound", from), sep = "_")

 	    }

 	    if (sub("_bound$", "", from) == sub("_free$", "", to)) {

-              k.candidate = paste("k", sub("_bound$", "_bound_free", from), sep="_")

+              k.candidate = paste("k", sub("_bound$", "_bound_free", from), sep = "_")

 	    }

             k.effective = intersect(model$parms, k.candidate)

             m[to, from] = ifelse(length(k.effective) > 0,

@@ -219,23 +219,27 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
       for (from in boxes) {

         for (to in boxes) {

           if (from == to) { # diagonal elements

-            k.candidate = paste("k", from, sep="_")

+            k.candidate = paste("k", from, sep = "_")

             m[from,to] = ifelse(k.candidate %in% model$parms,

                 paste("-", k.candidate), "0")

             if(grepl("_free", from)) { # add transfer to bound compartment for SFORB

-              m[from,to] = paste(m[from,to], "-", paste("k", from, "bound", sep="_"))

+              m[from,to] = paste(m[from,to], "-", paste("k", from, "bound", sep = "_"))

             }

             if(grepl("_bound", from)) { # add backtransfer to free compartment for SFORB

-              m[from,to] = paste("- k", from, "free", sep="_")

+              m[from,to] = paste("- k", from, "free", sep = "_")

             }

             m[from,to] = m[from,to]

           } else {          # off-diagonal elements

-            f.candidate = paste("f", from, "to", to, sep="_")

-            k.candidate = paste("k", from, to, sep="_")

-	    # SFORB with maximum use of formation fractions not implemented, see above

+            f.candidate = paste("f", from, "to", to, sep = "_")

+            k.candidate = paste("k", from, to, sep = "_")

+            # SFORB with maximum use of formation fractions not implemented, see above

             m[to, from] = ifelse(f.candidate %in% model$parms,

-              paste(f.candidate, " * k_", from, sep=""), 

+              paste(f.candidate, " * k_", from, sep = ""), 

               ifelse(k.candidate %in% model$parms, k.candidate, "0"))

+            # Special case: singular pathway and no sink

+            if (spec[[from]]$sink == FALSE && length(spec[[from]]$to) == 1 && to %in% spec[[from]]$to) {

+              m[to, from] = paste("k", from, sep = "_")

+            }

           }

         }

       }