Better support metabolites in `sawtooth`

Also, add more example code to make it easier to use
`one_box`, `sawtooth` and `pfm_degradation`.

However, for generating sawtooth curves with specified
output times, overlaying the output of several calls to
`mkinpredict` is probably still easier.

1 files changed, 26 insertions, 1 deletions

diff --git a/man/pfm_degradation.Rd b/man/pfm_degradation.Rd
index 81f2e81..163bcee 100644
--- a/man/pfm_degradation.Rd
+++ b/man/pfm_degradation.Rd
@@ -28,11 +28,36 @@ is calculated (SFO model).}
 
 \item{times}{The output times}
 }
+\value{
+A data frame containing the output times and the concentrations
+assuming initial concentrations of 1 for the parent and zero for
+metabolites, if any.
+}
 \description{
 Calculate a time course of relative concentrations based on an mkinmod model
 }
 \examples{
-head(pfm_degradation("SFO", DT50 = 10))
+# Simple example of an SFO decline curve
+sfo_out <- pfm_degradation("SFO", DT50 = 10)
+head(sfo_out)
+
+# Fictive example with a metabolite where we first generate an SFO-SFO model
+sfo_sfo <- mkinmod(
+  parent = mkinsub("SFO", to = "metabolite"),
+  metabolite = mkinsub("SFO"))
+
+sfo_sfo_out <- pfm_degradation(sfo_sfo,
+  parms = c(k_parent = 0.1, f_parent_to_metabolite = 0.5, k_metabolite = 0.02))
+
+plot(
+  sfo_sfo_out[, "time"],
+  sfo_sfo_out[, "parent"], type = "l",
+  xlab = "Time", ylab = "Relative concentration",
+  xlim = c(0, 100))
+lines(
+  sfo_sfo_out[, "time"],
+  sfo_sfo_out[, "metabolite"], lty = 2)
+
 }
 \author{
 Johannes Ranke