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, 33 insertions, 0 deletions

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") {