From 2e37905a7bf0d72751ee7326ef05a268989e49b2 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 7 Nov 2020 12:54:58 +0100
Subject: Create saem generic for fitting saemix models

The reasons for this decision were
- Creating an saemix generic in the saemix package caused problems with
  roxygen, because functions like saemix.plot.xy were documented in
  their help files as S3 methods, although explicitly exported with
  @export
- Creating an saemix generic in this package is possible, but would
  make it necessary to load samix with exclude = "saemix" in order to
  avoid overwriting the generic when loading saemix.
- The return object of such an saemix generic in this package cannot
  be an S3 class with class attribute c("saemix.mmkin", "SaemixObject")
  similar to nlme.mmkin, as saemix returns an S4 class.
- Extending the S4 class SaemixObject using simple inheritance to
  a class SaemixMmkinObject with additional slots did not work
  as expected.  When the initialize method was left untouched, it
  prevented creation of an SaemixMmkinObject even if it was based
  on an initialised SaemixObject, as the initialize method seems
  to always be called by new(). This could potentially be circumvented
  by a coerce method. If an alternative initialize method was
  used, an SaemixMmkinObject could be created. However, the methods
  written for SaemixObjects only worked in some instances, either
  because they checked for the class, and not for class inheritance
  (like compare.saemix), or because the initialize method was called
  for some reason. Therefore, the idea of creating a derived S4 class
  was abandoned.
- A side effect of this decision is that the introduction of the saem
  generic opens the possibility to use the same generic also for other
  backends like nlmixr with the SAEM algorithm.
---
 man/mkinpredict.Rd | 22 +++++-----------------
 1 file changed, 5 insertions(+), 17 deletions(-)

(limited to 'man/mkinpredict.Rd')

diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index f2799bf4..3a2939e1 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -6,19 +6,7 @@
 \alias{mkinpredict.mkinfit}
 \title{Produce predictions from a kinetic model using specific parameters}
 \usage{
-mkinpredict(
-  x,
-  odeparms,
-  odeini,
-  outtimes = seq(0, 120, by = 0.1),
-  solution_type = "deSolve",
-  use_compiled = "auto",
-  method.ode = "lsoda",
-  atol = 1e-08,
-  rtol = 1e-10,
-  map_output = TRUE,
-  ...
-)
+mkinpredict(x, odeparms, odeini, outtimes, ...)
 
 \method{mkinpredict}{mkinmod}(
   x,
@@ -30,8 +18,8 @@ mkinpredict(
   method.ode = "lsoda",
   atol = 1e-08,
   rtol = 1e-10,
-  na_stop = TRUE,
   map_output = TRUE,
+  na_stop = TRUE,
   ...
 )
 
@@ -65,6 +53,9 @@ observed variables, for example in the case of the SFORB model.}
 \item{outtimes}{A numeric vector specifying the time points for which model
 predictions should be generated.}
 
+\item{\dots}{Further arguments passed to the ode solver in case such a
+solver is used.}
+
 \item{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
@@ -89,9 +80,6 @@ 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.}
 
-\item{\dots}{Further arguments passed to the ode solver in case such a
-solver is used.}
-
 \item{na_stop}{Should it be an error if deSolve::ode returns NaN values}
 }
 \value{
-- 
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