- 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

1 files changed, 46 insertions, 0 deletions

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)

+}