From e959fde98f95f3595e01490b67892678bbcd1b27 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 7 May 2014 14:47:28 +0200
Subject: Fork the gmkin GUI from mkin. See ChangeLog for details

---
 R/transform_odeparms.R | 101 -------------------------------------------------
 1 file changed, 101 deletions(-)
 delete mode 100644 R/transform_odeparms.R

(limited to 'R/transform_odeparms.R')

diff --git a/R/transform_odeparms.R b/R/transform_odeparms.R
deleted file mode 100644
index a0c302f..0000000
--- a/R/transform_odeparms.R
+++ /dev/null
@@ -1,101 +0,0 @@
-# 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 isotropic 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 rates, fractions and tb also for FOMC, DFOP and HS models if 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 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
-      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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