# $Id$ # Copyright (C) 2010-2013 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) { # Set up container for transformed parameters transparms <- parms # Log transformation for rate constants index_k <- grep("^k_", names(transparms)) if (length(index_k) > 0) { transparms[index_k] <- log(parms[index_k]) } # Go through state variables and apply isotropic logratio transformation 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 transparms[indices_f] <- trans_f } } # Transform parameters also for FOMC, DFOP and HS models for (pname in c("alpha", "beta", "k1", "k2", "tb")) { if (!is.na(parms[pname])) { transparms[pname] <- log(parms[pname]) } } if (!is.na(parms["g"])) { g <- parms["g"] transparms["g"] <- ilr(c(g, 1- g)) } return(transparms) } backtransform_odeparms <- function(transparms, mod_vars) { # Set up container for backtransformed parameters parms <- transparms # Exponential transformation for rate constants index_k <- grep("^k_", names(parms)) if (length(index_k) > 0) { parms[index_k] <- exp(transparms[index_k]) } # Go through state variables and apply inverse isotropic 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 parms[indices_f] <- f } } # Transform parameters also for DFOP and HS models for (pname in c("alpha", "beta", "k1", "k2", "tb")) { if (!is.na(transparms[pname])) { parms[pname] <- exp(transparms[pname]) } } if (!is.na(transparms["g"])) { g <- transparms["g"] parms["g"] <- invilr(g)[1] } return(parms) }