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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, mkinmod,
transform_rates = TRUE,
transform_fractions = TRUE)
{
# We need the model specification for the names of the model
# variables and the information on the sink
spec = mkinmod$spec
# Set up container for transformed parameters
transparms <- numeric(0)
# Do not transform initial values for state variables
state.ini.optim <- parms[grep("_0$", names(parms))]
transparms[names(state.ini.optim)] <- state.ini.optim
# Log transformation for rate constants if requested
k <- parms[grep("^k_", names(parms))]
k__iore <- parms[grep("^k__iore_", names(parms))]
k <- c(k, k__iore)
if (length(k) > 0) {
if(transform_rates) {
transparms[paste0("log_", names(k))] <- log(k)
} else transparms[names(k)] <- k
}
# Do not transform exponents in IORE models
N <- parms[grep("^N", names(parms))]
transparms[names(N)] <- N
# Go through state variables and apply isometric logratio transformation to
# formation fractions if requested
mod_vars = names(spec)
for (box in mod_vars) {
f <- parms[grep(paste("^f", box, sep = "_"), names(parms))]
if (length(f) > 0) {
if(transform_fractions) {
if (spec[[box]]$sink) {
trans_f <- ilr(c(f, 1 - sum(f)))
trans_f_names <- paste("f", box, "ilr", 1:length(trans_f), sep = "_")
transparms[trans_f_names] <- trans_f
} else {
if (length(f) > 1) {
trans_f <- ilr(f)
trans_f_names <- paste("f", box, "ilr", 1:length(trans_f), sep = "_")
transparms[trans_f_names] <- trans_f
}
}
} else {
transparms[names(f)] <- f
}
}
}
# Transform also FOMC parameters alpha and beta, DFOP and HS rates k1 and k2
# and HS parameter tb if transformation of rates is requested
for (pname in c("alpha", "beta", "k1", "k2", "tb")) {
if (!is.na(parms[pname])) {
if (transform_rates) {
transparms[paste0("log_", pname)] <- log(parms[pname])
} else {
transparms[pname] <- parms[pname]
}
}
}
# DFOP parameter g is treated as a fraction
if (!is.na(parms["g"])) {
g <- parms["g"]
if (transform_fractions) {
transparms["g_ilr"] <- ilr(c(g, 1 - g))
} else {
transparms["g"] <- g
}
}
return(transparms)
}
backtransform_odeparms <- function(transparms, mkinmod,
transform_rates = TRUE,
transform_fractions = TRUE)
{
# We need the model specification for the names of the model
# variables and the information on the sink
spec = mkinmod$spec
# Set up container for backtransformed parameters
parms <- numeric(0)
# Do not transform initial values for state variables
state.ini.optim <- transparms[grep("_0$", names(transparms))]
parms[names(state.ini.optim)] <- state.ini.optim
# Exponential transformation for rate constants
if(transform_rates) {
trans_k <- transparms[grep("^log_k_", names(transparms))]
trans_k__iore <- transparms[grep("^log_k__iore_", names(transparms))]
trans_k = c(trans_k, trans_k__iore)
if (length(trans_k) > 0) {
k_names <- gsub("^log_k", "k", names(trans_k))
parms[k_names] <- exp(trans_k)
}
} else {
trans_k <- transparms[grep("^k_", names(transparms))]
parms[names(trans_k)] <- trans_k
trans_k__iore <- transparms[grep("^k__iore_", names(transparms))]
parms[names(trans_k__iore)] <- trans_k__iore
}
# Do not transform exponents in IORE models
N <- transparms[grep("^N", names(transparms))]
parms[names(N)] <- N
# Go through state variables and apply inverse isometric logratio transformation
mod_vars = names(spec)
for (box in mod_vars) {
# Get the names as used in the model
f_names = grep(paste("^f", box, sep = "_"), mkinmod$parms, value = TRUE)
# Get the formation fraction parameters
trans_f = transparms[grep(paste("^f", box, sep = "_"), names(transparms))]
if (length(trans_f) > 0) {
if(transform_fractions) {
f <- invilr(trans_f)
if (spec[[box]]$sink) {
parms[f_names] <- f[1:length(f)-1]
} else {
parms[f_names] <- f
}
} else {
parms[names(trans_f)] <- trans_f
}
}
}
# Transform parameters also for FOMC, DFOP and HS models
for (pname in c("alpha", "beta", "k1", "k2", "tb")) {
if (transform_rates) {
pname_trans = paste0("log_", pname)
if (!is.na(transparms[pname_trans])) {
parms[pname] <- exp(transparms[pname_trans])
}
} else {
if (!is.na(transparms[pname])) {
parms[pname] <- transparms[pname]
}
}
}
# DFOP parameter g is treated as a fraction
if (!is.na(transparms["g_ilr"])) {
g_ilr <- transparms["g_ilr"]
parms["g"] <- invilr(g_ilr)[1]
}
if (!is.na(transparms["g"])) {
parms["g"] <- transparms["g"]
}
return(parms)
}
# vim: set ts=2 sw=2 expandtab:
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