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.

2 files changed, 49 insertions, 1 deletions

diff --git a/man/one_box.Rd b/man/one_box.Rd
index 16f4859..cf8a91a 100644
--- a/man/one_box.Rd
+++ b/man/one_box.Rd
@@ -4,6 +4,7 @@
 \alias{one_box}
 \alias{one_box.numeric}
 \alias{one_box.character}
+\alias{one_box.mkinmod}
 \alias{one_box.mkinfit}
 \title{Create a time series of decline data}
 \usage{
@@ -13,6 +14,16 @@ one_box(x, ini, ..., t_end = 100, res = 0.01)
 
 \method{one_box}{character}(x, ini = 1, parms, ..., t_end = 100, res = 0.01)
 
+\method{one_box}{mkinmod}(
+  x,
+  ini = c(1, rep(0, length(x$diffs) - 1)),
+  odeparms,
+  solution_type = "deSolve",
+  ...,
+  t_end = 100,
+  res = 0.01
+)
+
 \method{one_box}{mkinfit}(x, ini = "model", ..., t_end = 100, res = 0.01)
 }
 \arguments{
@@ -35,6 +46,10 @@ all observed variables.}
 \item{res}{Resolution of the time series}
 
 \item{parms}{A named numeric vector containing the model parameters}
+
+\item{odeparms}{Will be passed to \link[mkin:mkinpredict]{mkinpredict}}
+
+\item{solution_type}{Will be passed to \link[mkin:mkinpredict]{mkinpredict}}
 }
 \value{
 An object of class \code{one_box}, inheriting from \link{ts}.
@@ -58,4 +73,12 @@ m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
 fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE)
 pred_2 <- one_box(fit_2, ini = "model")
 plot(pred_2)
+library(mkin)
+SFO_SFO <- mkinmod(
+  parent = mkinsub("SFO", to = "m1"),
+  m1 = mkinsub("SFO"))
+c_0 = c(parent = 100, m1 = 0)
+deg_parms = c(k_parent = 0.15, f_parent_to_m1 = 0.5, k_m1 = 0.01)
+sfo_sfo_box <- one_box(SFO_SFO, odeparms = deg_parms, ini = c_0)
+head(sfo_sfo_box)
 }
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