From 85cb80385bb26f40d1c1a40bbda457dd29c4cc23 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 4 Nov 2022 18:09:50 +0100
Subject: Make it easy to override maxsteps for lsoda

The hope was to be more successful in saemix fits, but I did not notice
an improvement (e.g. for a failing likelihood calculation with importance
sampling, where the error message suggested to increase maxsteps).
---
 R/mkinpredict.R | 49 ++++++++++++++++++++++++++-----------------------
 1 file changed, 26 insertions(+), 23 deletions(-)

(limited to 'R')

diff --git a/R/mkinpredict.R b/R/mkinpredict.R
index 9e6ba31f..0dc9cf55 100644
--- a/R/mkinpredict.R
+++ b/R/mkinpredict.R
@@ -1,40 +1,41 @@
 #' Produce predictions from a kinetic model using specific parameters
 #'
 #' This function produces a time series for all the observed variables in a
-#' kinetic model as specified by \code{\link{mkinmod}}, using a specific set of
+#' kinetic model as specified by [mkinmod], using a specific set of
 #' kinetic parameters and initial values for the state variables.
 #'
 #' @aliases mkinpredict mkinpredict.mkinmod mkinpredict.mkinfit
-#' @param x A kinetic model as produced by \code{\link{mkinmod}}, or a kinetic
-#'   fit as fitted by \code{\link{mkinfit}}. In the latter case, the fitted
-#'   parameters are used for the prediction.
+#' @param x A kinetic model as produced by [mkinmod], or a kinetic fit as
+#' fitted by [mkinfit]. In the latter case, the fitted parameters are used for
+#' the prediction.
 #' @param odeparms A numeric vector specifying the parameters used in the
-#'   kinetic model, which is generally defined as a set of ordinary
-#'   differential equations.
+#' kinetic model, which is generally defined as a set of ordinary differential
+#' equations.
 #' @param odeini A numeric vector containing the initial values of the state
-#'   variables of the model. Note that the state variables can differ from the
-#'   observed variables, for example in the case of the SFORB model.
+#' variables of the model. Note that the state variables can differ from the
+#' observed variables, for example in the case of the SFORB model.
 #' @param outtimes A numeric vector specifying the time points for which model
-#'   predictions should be generated.
+#' predictions should be generated.
 #' @param solution_type The method that should be used for producing the
-#'   predictions. This should generally be "analytical" if there is only one
-#'   observed variable, and usually "deSolve" in the case of several observed
-#'   variables. The third possibility "eigen" is faster but not applicable to
-#'   some models e.g.  using FOMC for the parent compound.
-#' @param method.ode The solution method passed via \code{\link{mkinpredict}}
-#'   to \code{\link{ode}} in case the solution type is "deSolve". The default
-#'   "lsoda" is performant, but sometimes fails to converge.
+#' predictions. This should generally be "analytical" if there is only one
+#' observed variable, and usually "deSolve" in the case of several observed
+#' variables. The third possibility "eigen" is faster but not applicable to
+#' some models e.g.  using FOMC for the parent compound.
+#' @param method.ode The solution method passed via [mkinpredict] to [ode]] in
+#' case the solution type is "deSolve". The default "lsoda" is performant, but
+#' sometimes fails to converge.
 #' @param use_compiled If set to \code{FALSE}, no compiled version of the
-#'   \code{\link{mkinmod}} model is used, even if is present.
-#' @param atol Absolute error tolerance, passed to \code{\link{ode}}. Default
-#'   is 1e-8, lower than in \code{\link{lsoda}}.
-#' @param rtol Absolute error tolerance, passed to \code{\link{ode}}. Default
-#'   is 1e-10, much lower than in \code{\link{lsoda}}.
+#' [mkinmod] model is used, even if is present.
+#' @param atol Absolute error tolerance, passed to [ode]. Default is 1e-8,
+#' lower than in [lsoda].
+#' @param rtol Absolute error tolerance, passed to [ode]. Default is 1e-10,
+#' much lower than in [lsoda].
+#' @param maxsteps Maximum number of steps, passed to [ode].
 #' @param map_output Boolean to specify if the output should list values for
 #'   the observed variables (default) or for all state variables (if set to
 #'   FALSE). Setting this to FALSE has no effect for analytical solutions,
 #'   as these always return mapped output.
-#' @param na_stop Should it be an error if deSolve::ode returns NaN values
+#' @param na_stop Should it be an error if [ode] returns NaN values
 #' @param \dots Further arguments passed to the ode solver in case such a
 #'   solver is used.
 #' @import deSolve
@@ -115,7 +116,7 @@ mkinpredict.mkinmod <- function(x,
   outtimes = seq(0, 120, by = 0.1),
   solution_type = "deSolve",
   use_compiled = "auto",
-  method.ode = "lsoda", atol = 1e-8, rtol = 1e-10,
+  method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, maxsteps = 20000,
   map_output = TRUE,
   na_stop = TRUE,
   ...)
@@ -183,6 +184,7 @@ mkinpredict.mkinmod <- function(x,
         method = method.ode,
         atol = atol,
         rtol = rtol,
+        maxsteps = maxsteps,
         ...
       )
     } else {
@@ -206,6 +208,7 @@ mkinpredict.mkinmod <- function(x,
         method = method.ode,
         atol = atol,
         rtol = rtol,
+        maxsteps = maxsteps,
         ...
       )
     }
-- 
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