From c504e823809aa8a299ed5326a22505f82d891ce5 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 16 Apr 2015 11:06:39 +0200
Subject: Update copyright header, improve documentation of solution_type
---
R/mkinfit.R | 29 +++++++++++++++++------------
R/mkinmod.R | 2 +-
R/mkinpredict.R | 2 +-
3 files changed, 19 insertions(+), 14 deletions(-)
(limited to 'R')
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 38f76674..5118519a 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2010-2014 Johannes Ranke
+# Copyright (C) 2010-2015 Johannes Ranke
# Portions of this code are copyright (C) 2013 Eurofins Regulatory AG
# Contact: jranke@uni-bremen.de
# The summary function is an adapted and extended version of summary.modFit
@@ -26,7 +26,7 @@ mkinfit <- function(mkinmod, observed,
state.ini = "auto",
fixed_parms = NULL,
fixed_initials = names(mkinmod$diffs)[-1],
- solution_type = "auto",
+ solution_type = c("auto", "analytical", "eigen", "deSolve"),
method.ode = "lsoda",
use_compiled = "auto",
method.modFit = c("Port", "Marq", "SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B"),
@@ -89,7 +89,7 @@ mkinfit <- function(mkinmod, observed,
" not used in the model")
}
- # Warn that the sum of formation fractions may exceed one they are not
+ # Warn that the sum of formation fractions may exceed one if they are not
# fitted in the transformed way
if (mkinmod$use_of_ff == "max" & transform_fractions == FALSE) {
warning("The sum of formation fractions may exceed one if you do not use ",
@@ -112,7 +112,7 @@ mkinfit <- function(mkinmod, observed,
stop("Fixing formation fractions is not supported when using the ilr ",
"transformation.")
}
- }
+ }
# Set initial parameter values, including a small increment (salt)
# to avoid linear dependencies (singular matrix) in Eigenvalue based solutions
@@ -208,8 +208,9 @@ mkinfit <- function(mkinmod, observed,
# Decide if the solution of the model can be based on a simple analytical
# formula, the spectral decomposition of the matrix (fundamental system)
# or a numeric ode solver from the deSolve package
- if (!solution_type %in% c("auto", "analytical", "eigen", "deSolve"))
- stop("solution_type must be auto, analytical, eigen or de Solve")
+ # Prefer deSolve over eigen if a compiled model is present and use_compiled
+ # is not set to FALSE
+ solution_type = match.arg(solution_type)
if (solution_type == "analytical" && length(mkinmod$spec) > 1)
stop("Analytical solution not implemented for models with metabolites.")
if (solution_type == "eigen" && !is.matrix(mkinmod$coefmat))
@@ -218,13 +219,17 @@ mkinfit <- function(mkinmod, observed,
if (length(mkinmod$spec) == 1) {
solution_type = "analytical"
} else {
- if (is.matrix(mkinmod$coefmat)) {
- solution_type = "eigen"
- if (max(observed$value, na.rm = TRUE) < 0.1) {
- stop("The combination of small observed values (all < 0.1) and solution_type = eigen is error-prone")
- }
- } else {
+ if (!is.null(mkinmod$compiled) & use_compiled[1] != FALSE) {
solution_type = "deSolve"
+ } else {
+ if (is.matrix(mkinmod$coefmat)) {
+ solution_type = "eigen"
+ if (max(observed$value, na.rm = TRUE) < 0.1) {
+ stop("The combination of small observed values (all < 0.1) and solution_type = eigen is error-prone")
+ }
+ } else {
+ solution_type = "deSolve"
+ }
}
}
}
diff --git a/R/mkinmod.R b/R/mkinmod.R
index 37cd02b4..e73c56c6 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2010-2014 Johannes Ranke {{{
+# Copyright (C) 2010-2015 Johannes Ranke {{{
# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
diff --git a/R/mkinpredict.R b/R/mkinpredict.R
index 864eefbe..3e3ca0bf 100644
--- a/R/mkinpredict.R
+++ b/R/mkinpredict.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2010-2014 Johannes Ranke
+# Copyright (C) 2010-2015 Johannes Ranke
# Some lines in this code are copyright (C) 2013 Eurofins Regulatory AG
# Contact: jranke@uni-bremen.de
--
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