More work on the examples vignette

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@65 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

1 files changed, 16 insertions, 8 deletions

diff --git a/R/mkinmod.R b/R/mkinmod.R
index 5d8271a..adfd9ea 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -22,6 +22,12 @@ mkinmod <- function(..., use_of_ff = "min")
 {

   spec <- list(...)

   obs_vars <- names(spec)

+

+  # Check if any of the names of the observed variables contains any other

+  for (obs_var in obs_vars) {

+    if (length(grep(obs_var, obs_vars)) > 1) stop("Sorry, variable names can not contain each other")

+  }

+

   if (!use_of_ff %in% c("min", "max"))

     stop("The use of formation fractions 'use_of_ff' can only be 'min' or 'max'")

 

@@ -43,7 +49,7 @@ mkinmod <- function(..., use_of_ff = "min")
         "Only constant formation fractions over time are implemented.",

         "Depending on the reason for the time dependence of degradation",

         "this may be unrealistic. You may want to consider using the",

-	"SFORB model",

+        "SFORB model",

         sep="\n")

       warning(message)

     } else message <- "ok"

@@ -84,12 +90,11 @@ mkinmod <- function(..., use_of_ff = "min")
   {

     # Get the name of the box(es) we are working on for the decline term(s)

     box_1 = map[[varname]][[1]] # This is the only box unless type is SFORB

+    # Turn on sink if this is not explicitly excluded by the user by

+    # specifying sink=FALSE

+    if(is.null(spec[[varname]]$sink)) spec[[varname]]$sink <- TRUE

     if(spec[[varname]]$type %in% c("SFO", "SFORB")) { # {{{ Add SFO or SFORB decline term

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

-	# Turn on sink if this is not explicitly excluded by the user by

-	# specifying sink=FALSE

-	if(is.null(spec[[varname]]$sink)) spec[[varname]]$sink <- TRUE

-

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

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

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

@@ -103,7 +108,7 @@ mkinmod <- function(..., use_of_ff = "min")
         parms <- c(parms, k_compound)

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

       }

-    }#}}}

+    } #}}}

     if(spec[[varname]]$type == "FOMC") { # {{{ Add FOMC decline term

       # From p. 53 of the FOCUS kinetics report

       decline_term <- paste("(alpha/beta) * ((time/beta) + 1)^-1 *", box_1)

@@ -132,7 +137,7 @@ mkinmod <- function(..., use_of_ff = "min")
         reversible_binding_term_2 <- paste("+", k_free_bound, "*", box_1, "-",

           k_bound_free, "*", box_2)

       } else { # Use formation fractions also for the free compartment

-	stop("The maximum use of formation fractions is not supported for SFORB models")

+        stop("The maximum use of formation fractions is not supported for SFORB models")

         # 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

@@ -167,6 +172,9 @@ mkinmod <- function(..., use_of_ff = "min")
           diffs[[target_box]] <- paste(diffs[[target_box]], "+", 

             k_from_to, "*", origin_box)

         } else {

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

+            stop("Turning off the sink when using formation fractions is not supported")

+          }

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

           parms <- c(parms, fraction_to_target)

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

@@ -240,4 +248,4 @@ mkinmod <- function(..., use_of_ff = "min")
   class(model) <- "mkinmod"

   return(model)

 }

-# vim: set foldmethod=marker:

+# vim: set foldmethod=marker ts=2 sw=2 expandtab: