IORE working for parent and metabolites, introduce mkinsub

2 files changed, 50 insertions, 0 deletions

diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index c40dff83..a16ed177 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -216,6 +216,12 @@ mkinfit(mkinmod, observed,
   Gao). A similar implemention can also be found in CAKE 2.0, which is the
   other GUI derivative of mkin, sponsored by Syngenta.
 }
+\note{
+  When using the "IORE" submodel for metabolites, fitting with 
+  "transform_rates = TRUE" (the default) often leads to failures of the
+  numerical ODE solver. In this situation it may help to switch off the
+  internal rate transformation.
+}
 \author{
   Johannes Ranke
 }
diff --git a/man/mkinsub.Rd b/man/mkinsub.Rd
new file mode 100644
index 00000000..637a671c
--- /dev/null
+++ b/man/mkinsub.Rd
@@ -0,0 +1,44 @@
+\name{mkinsub}
+\alias{mkinsub}
+\title{
+  Function to set up a kinetic submodel for one state variable
+}
+\description{
+  This is a convenience function to set up the lists used as arguments for 
+  \code{\link{mkinmod}}.
+}
+\usage{
+mkinsub(type, to = NULL, sink = TRUE)
+}
+\arguments{
+  \item{type}{
+    Character vector of length one to specify the submodel type. See 
+    \code{\link{mkinmod}} for the list of allowed submodel names.
+  }
+  \item{to}{
+    Vector of the names of the state variable to which a transformation 
+    shall be included in the model.
+  }
+  \item{sink}{
+    Should a pathway to sink be included in the model in addition to the 
+    pathways to other state variables?
+  }
+}
+\value{
+  A list for use with \code{\link{mkinmod}}.
+}
+\author{
+  Johannes Ranke
+}
+\examples{
+# One parent compound, one metabolite, both single first order.
+SFO_SFO <- mkinmod(
+  parent = list(type = "SFO", to = "m1"),
+  m1 = list(type = "SFO"))
+
+# The same model using mkinsub
+SFO_SFO.2 <- mkinmod(
+  parent = mkinsub("SFO", "m1"),
+  m1 = mkinsub("SFO"))
+}
+