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Diffstat (limited to 'R/mkinpredict.R')
-rw-r--r-- | R/mkinpredict.R | 121 |
1 files changed, 0 insertions, 121 deletions
diff --git a/R/mkinpredict.R b/R/mkinpredict.R deleted file mode 100644 index 14efc56..0000000 --- a/R/mkinpredict.R +++ /dev/null @@ -1,121 +0,0 @@ -# Copyright (C) 2010-2014 Johannes Ranke -# Some lines in this code are copyright (C) 2013 Eurofins Regulatory AG -# Contact: jranke@uni-bremen.de - -# This file is part of the R package mkin - -# mkin is free software: you can redistribute it and/or modify it under the -# terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see <http://www.gnu.org/licenses/> - -mkinpredict <- function(mkinmod, odeparms, odeini, - outtimes, solution_type = "deSolve", - method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, - map_output = TRUE, ...) { - - # Get the names of the state variables in the model - mod_vars <- names(mkinmod$diffs) - - # Order the inital values for state variables if they are named - if (!is.null(names(odeini))) { - odeini <- odeini[mod_vars] - } - - # Create function for evaluation of expressions with ode parameters and initial values - evalparse <- function(string) - { - eval(parse(text=string), as.list(c(odeparms, odeini))) - } - - # Create a function calculating the differentials specified by the model - # if necessary - if (solution_type == "analytical") { - parent.type = names(mkinmod$map[[1]])[1] - parent.name = names(mkinmod$diffs)[[1]] - o <- switch(parent.type, - SFO = SFO.solution(outtimes, - evalparse(parent.name), - ifelse(mkinmod$use_of_ff == "min", - evalparse(paste("k", parent.name, "sink", sep="_")), - evalparse(paste("k", parent.name, sep="_")))), - FOMC = FOMC.solution(outtimes, - evalparse(parent.name), - evalparse("alpha"), evalparse("beta")), - DFOP = DFOP.solution(outtimes, - evalparse(parent.name), - evalparse("k1"), evalparse("k2"), - evalparse("g")), - HS = HS.solution(outtimes, - evalparse(parent.name), - evalparse("k1"), evalparse("k2"), - evalparse("tb")), - SFORB = SFORB.solution(outtimes, - evalparse(parent.name), - evalparse(paste("k", parent.name, "bound", sep="_")), - evalparse(paste("k", sub("free", "bound", parent.name), "free", sep="_")), - evalparse(paste("k", parent.name, "sink", sep="_"))) - ) - out <- data.frame(outtimes, o) - names(out) <- c("time", sub("_free", "", parent.name)) - } - if (solution_type == "eigen") { - coefmat.num <- matrix(sapply(as.vector(mkinmod$coefmat), evalparse), - nrow = length(mod_vars)) - e <- eigen(coefmat.num) - c <- solve(e$vectors, odeini) - f.out <- function(t) { - e$vectors %*% diag(exp(e$values * t), nrow=length(mod_vars)) %*% c - } - o <- matrix(mapply(f.out, outtimes), - nrow = length(mod_vars), ncol = length(outtimes)) - out <- data.frame(outtimes, t(o)) - names(out) <- c("time", mod_vars) - } - if (solution_type == "deSolve") { - mkindiff <- function(t, state, parms) { - - time <- t - diffs <- vector() - for (box in names(mkinmod$diffs)) - { - diffname <- paste("d", box, sep="_") - diffs[diffname] <- with(as.list(c(time, state, parms)), - eval(parse(text=mkinmod$diffs[[box]]))) - } - return(list(c(diffs))) - } - out <- ode( - y = odeini, - times = outtimes, - func = mkindiff, - parms = odeparms, - method = method.ode, - atol = atol, - rtol = rtol, - ... - ) - } - if (map_output) { - # Output transformation for models with unobserved compartments like SFORB - out_mapped <- data.frame(time = out[,"time"]) - for (var in names(mkinmod$map)) { - if((length(mkinmod$map[[var]]) == 1) || solution_type == "analytical") { - out_mapped[var] <- out[, var] - } else { - out_mapped[var] <- rowSums(out[, mkinmod$map[[var]]]) - } - } - return(out_mapped) - } else { - return(out) - } -} |