From d3df16102c5ed4bf9182b4f1893561e99eaed166 Mon Sep 17 00:00:00 2001
From: jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date: Tue, 3 Apr 2012 05:17:54 +0000
Subject: - Separated model prediction out into a separate function - Created
 separate functions for parameter transformations (not documented yet) -
 Fitting of analytical models works - SFO_SFO model works, complex models do
 not at the moment - summary.mkinfit not operational at the moment

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@21 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
---
 R/transform_odeparms.R | 46 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 R/transform_odeparms.R

(limited to 'R/transform_odeparms.R')

diff --git a/R/transform_odeparms.R b/R/transform_odeparms.R
new file mode 100644
index 00000000..4b8bfd14
--- /dev/null
+++ b/R/transform_odeparms.R
@@ -0,0 +1,46 @@
+transform_odeparms <- function(odeparms, mod_vars) {
+  # Transform rate constants and formation fractions
+  transparms <- odeparms
+  # Exponential transformation for rate constants
+  index_k <- grep("^k_", names(odeparms))
+  if (length(index_k) > 0) {
+    transparms[index_k] <- exp(odeparms[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(odeparms))
+    f_names <- grep(paste("^f", box, sep = "_"), names(odeparms), value = TRUE)
+    n_paths <- length(indices_f)
+    if (n_paths > 0) {
+      f <- invilr(odeparms[indices_f])[1:n_paths] # We do not need the last component
+      names(f) <- f_names
+      transparms[indices_f] <- f
+    }
+  }
+  return(transparms)
+}
+
+backtransform_odeparms <- function(transparms, mod_vars) {
+  # Transform rate constants and formation fractions
+  odeparms <- transparms
+  # Log transformation for rate constants
+  index_k <- grep("^k_", names(transparms))
+  if (length(index_k) > 0) {
+    odeparms[index_k] <- log(transparms[index_k])
+  }
+
+  # Go through state variables and apply 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) {
+      trans_f <- transparms[indices_f]
+      f <- ilr(c(trans_f, 1 - sum(trans_f)))
+      names(f) <- f_names
+      odeparms[indices_f] <- f
+    }
+  }
+  return(odeparms)
+}
-- 
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