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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/>
transform_odeparms <- function(parms, mod_vars,
transform_rates = TRUE,
transform_fractions = TRUE)
{
# Set up container for transformed parameters
transparms <- parms
# Log transformation for rate constants if requested
index_k <- grep("^k_", names(transparms))
if (length(index_k) > 0) {
if(transform_rates) transparms[index_k] <- log(parms[index_k])
else transparms[index_k] <- parms[index_k]
}
# Go through state variables and apply isometric logratio transformation if requested
for (box in mod_vars) {
indices_f <- grep(paste("^f", box, sep = "_"), names(parms))
f_names <- grep(paste("^f", box, sep = "_"), names(parms), value = TRUE)
n_paths <- length(indices_f)
if (n_paths > 0) {
f <- parms[indices_f]
trans_f <- ilr(c(f, 1 - sum(f)))
names(trans_f) <- f_names
if(transform_fractions) transparms[indices_f] <- trans_f
else transparms[indices_f] <- f
}
}
# Transform also FOMC parameters alpha and beta, DFOP and HS rates k1 and k2
# and HS parameter tb if transformation of rates is requested
for (pname in c("alpha", "beta", "k1", "k2", "tb")) {
if (!is.na(parms[pname])) {
transparms[pname] <- ifelse(transform_rates, log(parms[pname]), parms[pname])
transparms[pname] <- ifelse(transform_rates, log(parms[pname]), parms[pname])
}
}
if (!is.na(parms["g"])) {
g <- parms["g"]
transparms["g"] <- ifelse(transform_fractions, ilr(c(g, 1 - g)), g)
}
return(transparms)
}
backtransform_odeparms <- function(transparms, mod_vars,
transform_rates = TRUE,
transform_fractions = TRUE)
{
# Set up container for backtransformed parameters
parms <- transparms
# Exponential transformation for rate constants
index_k <- grep("^k_", names(parms))
if (length(index_k) > 0) {
if(transform_rates) parms[index_k] <- exp(transparms[index_k])
else parms[index_k] <- transparms[index_k]
}
# Go through state variables and apply inverse isometric logratio transformation
for (box in mod_vars) {
indices_f <- grep(paste("^f", box, sep = "_"), names(transparms))
f_names <- grep(paste("^f", box, sep = "_"), names(transparms), value = TRUE)
n_paths <- length(indices_f)
if (n_paths > 0) {
f <- invilr(transparms[indices_f])[1:n_paths] # We do not need the last component
names(f) <- f_names
if(transform_fractions) parms[indices_f] <- f
else parms[indices_f] <- transparms[indices_f]
}
}
# Transform parameters also for FOMC, DFOP and HS models
for (pname in c("alpha", "beta", "k1", "k2", "tb")) {
if (!is.na(transparms[pname])) {
parms[pname] <- ifelse(transform_rates, exp(transparms[pname]), transparms[pname])
}
}
if (!is.na(transparms["g"])) {
g <- transparms["g"]
parms["g"] <- ifelse(transform_fractions, invilr(g)[1], g)
}
return(parms)
}
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