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.

8 files changed, 129 insertions, 23 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 696eb3e..b0eeac3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
 Version: 0.6.5
-Date: 2026-06-22
+Date: 2026-09-10
 Authors@R: c(
   person("Johannes Ranke", email = "johannes.ranke@agroscope.admin.ch",
     role = c("aut", "cre"),
@@ -25,5 +25,6 @@ LazyLoad: true
 LazyData: true
 Encoding: UTF-8
 URL: https://pkgdown.jrwb.de/pfm, https://github.com/jranke/pfm, http://jranke.github.io/pfm/
+Additional_repositories: https://agroscope-ch.r-universe.dev, https://jranke.r-universe.dev
 Roxygen: list(markdown = TRUE, r6 = TRUE)
 Config/roxygen2/version: 8.0.0
diff --git a/NAMESPACE b/NAMESPACE
index 499e471..3507706 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -6,6 +6,7 @@ S3method(max_twa,mkinfit)
 S3method(max_twa,one_box)
 S3method(one_box,character)
 S3method(one_box,mkinfit)
+S3method(one_box,mkinmod)
 S3method(one_box,numeric)
 S3method(plot,TOXSWA_cwa)
 S3method(plot,one_box)
diff --git a/NEWS.md b/NEWS.md
index 516ac58..91319ec 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,7 @@
 ## version 0.6.5
 
+- Add a `one_box` method for `mkinmod` objects to facilitate generating `sawtooth` curves also for metabolites
+- R/pfm_degradation.R: Fix using an mkinmod model and add an SFO-SFO example
 - R/PEC_sw_drift.R: Support specifying units for distances and widths using the units package.
 - R/TOXSWA_cwa.R: Adapt to readr (>= 2.2.0) requiring to wrap literal input as used for reading .out files with I().
 - R/PEC_sw_drainage_UK.R: Create a function `drainage_date_UK` that does not only respect the beginning of the drainage period on 1 October, but also the end of the drainage period on 30 April, and use it for determining the degradation time. Applications early in the year before 1 May will now correctly be calculated without degradation time.
diff --git a/R/pfm_degradation.R b/R/pfm_degradation.R
index 832a797..63a6e19 100644
--- a/R/pfm_degradation.R
+++ b/R/pfm_degradation.R
@@ -9,21 +9,48 @@
 #' @param years For how many years should the degradation be predicted?
 #' @param step_days What step size in days should the output have?
 #' @param times The output times
+#' @return A data frame containing the output times and the concentrations
+#'   assuming initial concentrations of 1 for the parent and zero for
+#'   metabolites, if any.
 #' @export
 #' @author Johannes Ranke
 #' @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)
+#'
 pfm_degradation <- function(model = "SFO",
   DT50 = 1000, parms = c(k_parent = log(2)/DT50),
   years = 1, step_days = 1,
   times = seq(0, years * 365, by = step_days))
 {
-  if (model %in% c("SFO", "FOMC", "DFOP", "HS", "IORE")) {
-    model <- mkinmod(parent = list(type = model))
+  if (!inherits(model, "mkinmod")) {
+    if (model[1] %in% c("SFO", "FOMC", "DFOP", "HS", "IORE")) {
+      model <- mkinmod(parent = list(type = model))
+    } else {
+      stop("Please specify the model with a suitable name or an mkinmod object")
+    }
   }
   initial_state = c(1, rep(0, length(model$diffs) - 1))
   names(initial_state) <- names(model$diffs)
-  time_course <- mkinpredict(model, odeparms = parms, 
+  time_course <- mkinpredict(model, odeparms = parms,
     odeini = initial_state,
     outtimes = times,
     solution_type = ifelse(length(model$spec) == 1, "analytical", "deSolve"))
diff --git a/R/twa.R b/R/twa.R
index 0506334..8ca490d 100644
--- a/R/twa.R
+++ b/R/twa.R
@@ -82,8 +82,41 @@ one_box.character <- function(x, ini = 1, parms, ...,
 }
 
 #' @rdname one_box
+#' @param odeparms Will be passed to [mkinpredict]
+#' @param solution_type Will be passed to [mkinpredict]
 #' @importFrom mkin mkinpredict
 #' @export
+#' @examples
+#' 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)
+one_box.mkinmod <- function(x,
+  ini = c(1, rep(0, length(x$diffs) - 1)),
+  odeparms,
+  solution_type = "deSolve",
+  ...,
+  t_end = 100, res = 0.01)
+{
+
+  # Set names for initial amounts to be compatible with the model
+  if (is.null(names(ini))) names(ini) <- names(x$diffs)
+
+  t_out = seq(0, t_end, by = res)
+
+  tmp <- mkinpredict(x, odeparms = odeparms, odeini = ini,
+    outtimes = t_out, solution_type = solution_type)[, -1, drop = FALSE]
+  result <- ts(tmp, 0, t_end, frequency = 1/res)
+  class(result) <- c("one_box", "ts")
+  return(result)
+}
+
+#' @rdname one_box
+#' @export
 one_box.mkinfit <- function(x, ini = "model", ..., t_end = 100, res = 0.01) {
   fit <- x
   if (ini[1] == "model") {
diff --git a/log/check.log b/log/check.log
index 3c0c083..0897357 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,12 +1,12 @@
-* using log directory ‘/home/f80868656/projects/pfm/pfm.Rcheck’
-* using R version 4.6.0 (2026-04-24)
+* using log directory ‘/home/jranke/git/pfm/pfm.Rcheck’
+* using R version 4.6.1 (2026-06-24)
 * using platform: x86_64-pc-linux-gnu
 * R was compiled by
-    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
-    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
-* running under: Ubuntu 24.04.4 LTS
+    x86_64-linux-gnu-gcc (Debian 14.2.0-19) 14.2.0
+    GNU Fortran (Debian 14.2.0-19) 14.2.0
+* running under: Debian GNU/Linux 13 (trixie)
 * using session charset: UTF-8
-* current time: 2026-06-22 16:48:14 UTC
+* current time: 2026-09-10 10:31:00 UTC
 * using options ‘--no-tests --as-cran’
 * checking for file ‘pfm/DESCRIPTION’ ... OK
 * checking extension type ... Package
@@ -23,9 +23,9 @@
 * checking for sufficient/correct file permissions ... OK
 * checking whether package ‘pfm’ can be installed ... OK
 * checking installed package size ... INFO
-  installed size is 10.4Mb
+  installed size is 10.3Mb
   sub-directories of 1Mb or more:
-    testdata  10.0Mb
+    testdata   9.9Mb
 * checking package directory ... OK
 * checking for future file timestamps ... OK
 * checking DESCRIPTION meta-information ... OK
@@ -60,20 +60,14 @@
 * checking data for non-ASCII characters ... OK
 * checking LazyData ... OK
 * checking data for ASCII and uncompressed saves ... OK
-* checking examples ... [11s/10s] OK
+* checking examples ... [10s/10s] OK
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking PDF version of manual ... OK
-* checking HTML version of manual ... NOTE
-Skipping checking HTML validation: no command 'tidy' found.
-Please obtain a recent version of HTML Tidy by downloading a binary
-release or compiling the source code from <https://www.html-tidy.org/>.
+* checking HTML version of manual ... OK
 * checking for non-standard things in the check directory ... OK
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 1 NOTE
-See
-  ‘/home/f80868656/projects/pfm/pfm.Rcheck/00check.log’
-for details.
+Status: OK
 
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