From 5b3daf393831acc4099e1bde3fe4527993529d74 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 18 Oct 2017 11:28:39 +0200
Subject: Version 3.2

---
 CakeHelpers.R | 118 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 118 insertions(+)
 create mode 100755 CakeHelpers.R

(limited to 'CakeHelpers.R')

diff --git a/CakeHelpers.R b/CakeHelpers.R
new file mode 100755
index 0000000..5af51cc
--- /dev/null
+++ b/CakeHelpers.R
@@ -0,0 +1,118 @@
+# $Id$
+# Some of the CAKE R modules are based on mkin, 
+# Developed by Tessella Ltd for Syngenta: Copyright (C) 2011-2016 Syngenta
+# Tessella Project Reference: 6245, 7247, 8361, 7414
+
+#    The CAKE R modules are 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/>.
+
+# Shifts parameters slightly away from boundaries specified in "lower" and 
+# "upper" (to avoid computational issues after parameter transforms in modFit).
+ShiftAwayFromBoundaries <- function(parameters, lower, upper) {
+  parametersOnLowerBound = which(parameters == lower)
+  parameters[parametersOnLowerBound] <- parameters[parametersOnLowerBound] * (1 + .Machine$double.eps) + .Machine$double.xmin
+
+  parametersOnUpperBound = which(parameters == upper)
+  parameters[parametersOnUpperBound] <- parameters[parametersOnUpperBound] * (1 - .Machine$double.neg.eps) - .Machine$double.xmin
+
+  return(parameters)
+}
+
+# Adjusts stated initial values to put into the ODE solver.
+#
+# odeini: The initial values to adjust (in the form that would be fed into the ode function).
+# cake.model: The expression of the model that we are solving.
+# odeparms: The parameters for the ODE (in the form that would be fed into the ode function).
+#
+# Returns: Adjusted initial values.
+AdjustOdeInitialValues <- function(odeini, cake.model, odeparms) {
+  odeini.names <- names(odeini)
+  
+  for (ini.name in odeini.names) {
+    # For DFOP metabolites in two compartments, need to calculate some initial conditions for the ODEs.
+    if (!(ini.name %in% names(cake.model$diffs))){
+      subcompartment1.name <- paste(ini.name, "1", sep="_")
+      subcompartment2.name <- paste(ini.name, "2", sep="_")
+      
+      if (subcompartment1.name %in% names(cake.model$diffs) && subcompartment2.name %in% names(cake.model$diffs)){
+        g.parameter.name = paste("g", ini.name, sep="_")
+        
+        odeini[[subcompartment1.name]] <- odeini[[ini.name]] * odeparms[[g.parameter.name]]   
+        odeini[[subcompartment2.name]] <- odeini[[ini.name]] * (1 - odeparms[[g.parameter.name]])
+      }
+    }
+  }
+  
+  # It is important that these parameters are stated in the same order as the differential equations.
+  return(odeini[names(cake.model$diffs)])
+}
+
+# Post-processes the output from the ODE solver (or analytical process), including recombination of sub-compartments.
+#
+# odeoutput: The output of the ODE solver.
+# cake.model: The expression of the model that we are solving.
+# atol: The tolerance to which the solution has been calculated.
+#
+# Returns: Post-processed/transformed ODE output.
+PostProcessOdeOutput <- function(odeoutput, cake.model, atol) {
+  out_transformed <- data.frame(time = odeoutput[, "time"])
+  
+  # Replace values that are incalculably small with 0.
+  for (col.name in colnames(odeoutput)) {
+    if (col.name == "time") {
+      next
+    }
+    
+    # If we have non-NaN, positive outputs...
+    if (length(odeoutput[, col.name][!is.nan(odeoutput[, col.name]) && odeoutput[, col.name] > 0]) > 0) {
+      # ...then replace the NaN outputs.
+      odeoutput[, col.name][is.nan(odeoutput[, col.name])] <- 0
+    }
+    
+    # Round outputs smaller than the used tolerance down to 0.
+    odeoutput[, col.name][odeoutput[, col.name] < atol] <- 0
+  }
+  
+  # Re-combine sub-compartments (if required)
+  for (compartment.name in names(cake.model$map)) {
+    if (length(cake.model$map[[compartment.name]]) == 1) {
+      out_transformed[compartment.name] <- odeoutput[, compartment.name]
+    } else {
+      out_transformed[compartment.name] <- rowSums(odeoutput[, cake.model$map[[compartment.name]]])
+    }
+  }
+  
+  return(out_transformed)
+}
+
+# Reorganises data in a wide format to a long format.
+#
+# wide_data: The data in wide format.
+# time: The name of the time variable in wide_data (default "t").
+#
+# Returns: Reorganised data.
+wide_to_long <- function(wide_data, time = "t") {
+  colnames <- names(wide_data)
+  
+  if (!(time %in% colnames)) {
+    stop("The data in wide format have to contain a variable named ", time, ".")
+  }
+  
+  vars <- subset(colnames, colnames != time)
+  n <- length(colnames) - 1
+  long_data <- data.frame(name = rep(vars, each = length(wide_data[[time]])), 
+                          time = as.numeric(rep(wide_data[[time]], n)), value = as.numeric(unlist(wide_data[vars])), 
+                          row.names = NULL)
+  
+  return(long_data)
+}
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