From c504e823809aa8a299ed5326a22505f82d891ce5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke 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 -- cgit v1.2.1