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# Copyright (C) 2010-2014 Johannes Ranke
# 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/>
if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "value_mean"))
mkinerrmin <- function(fit, alpha = 0.05)
{
parms.optim <- fit$par
kinerrmin <- function(errdata, n.parms) {
means.mean <- mean(errdata$value_mean, na.rm = TRUE)
df = length(errdata$value_mean) - n.parms
err.min <- sqrt((1 / qchisq(1 - alpha, df)) *
sum((errdata$value_mean - errdata$value_pred)^2)/(means.mean^2))
return(list(err.min = err.min, n.optim = n.parms, df = df))
}
means <- aggregate(value ~ time + name, data = fit$observed, mean, na.rm=TRUE)
errdata <- merge(means, fit$predicted, by = c("time", "name"),
suffixes = c("_mean", "_pred"))
errdata <- errdata[order(errdata$time, errdata$name), ]
# Remove values at time zero for variables whose value for state.ini is fixed,
# as these will not have any effect in the optimization and should therefore not
# be counted as degrees of freedom.
fixed_initials = gsub("_0$", "", rownames(subset(fit$fixed, type = "state")))
errdata <- subset(errdata, !(time == 0 & name %in% fixed_initials))
n.optim.overall <- length(parms.optim)
errmin.overall <- kinerrmin(errdata, n.optim.overall)
errmin <- data.frame(err.min = errmin.overall$err.min,
n.optim = errmin.overall$n.optim, df = errmin.overall$df)
rownames(errmin) <- "All data"
# The degrees of freedom are counted according to FOCUS kinetics (2011, p. 164)
for (obs_var in fit$obs_vars)
{
errdata.var <- subset(errdata, name == obs_var)
# Check if initial value is optimised
n.initials.optim <- length(grep(paste(obs_var, ".*", "_0", sep=""), names(parms.optim)))
# Rate constants and IORE exponents are attributed to the source variable
n.k.optim <- length(grep(paste("^k", obs_var, sep="_"), names(parms.optim)))
n.k.optim <- n.k.optim + length(grep(paste("^log_k", obs_var, sep="_"),
names(parms.optim)))
n.k.iore.optim <- length(grep(paste("^k.iore", obs_var, sep="_"), names(parms.optim)))
n.k.iore.optim <- n.k.iore.optim + length(grep(paste("^log_k.iore", obs_var,
sep = "_"),
names(parms.optim)))
n.N.optim <- length(grep(paste("^N", obs_var, sep="_"), names(parms.optim)))
n.ff.optim <- 0
# Formation fractions are attributed to the target variable, so look
# for source compartments with formation fractions
for (source_var in fit$obs_vars) {
n.ff.source = length(grep(paste("^f", source_var, sep = "_"),
names(parms.optim)))
n.paths.source = length(fit$mkinmod$spec[[source_var]]$to)
for (target_var in fit$mkinmod$spec[[source_var]]$to) {
if (obs_var == target_var) {
n.ff.optim <- n.ff.optim + n.ff.source/n.paths.source
}
}
}
n.optim <- sum(n.initials.optim, n.k.optim, n.k.iore.optim, n.N.optim, n.ff.optim)
# FOMC, DFOP and HS parameters are only counted if we are looking at the
# first variable in the model which is always the source variable
if (obs_var == fit$obs_vars[[1]]) {
special_parms = c("alpha", "log_alpha", "beta", "log_beta",
"k1", "log_k1", "k2", "log_k2",
"g", "g_ilr", "tb", "log_tb")
n.optim <- n.optim + length(intersect(special_parms, names(parms.optim)))
}
# Calculate and add a line to the dataframe holding the results
errmin.tmp <- kinerrmin(errdata.var, n.optim)
errmin[obs_var, c("err.min", "n.optim", "df")] <- errmin.tmp
}
return(errmin)
}
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