From a69bf39427ff4f93eebdc8bceacb8174ff13c085 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 14 Jul 2014 19:07:54 +0200
Subject: Nearly complete support for IORE, pending mkinerrmin

---
 man/mkinmod.Rd     | 26 +++++++++++++++++++++-----
 man/mkinpredict.Rd | 19 ++++++++++++-------
 2 files changed, 33 insertions(+), 12 deletions(-)

(limited to 'man')

diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
index 63087d49..e6749ded 100644
--- a/man/mkinmod.Rd
+++ b/man/mkinmod.Rd
@@ -4,9 +4,13 @@
   Function to set up a kinetic model with one or more state variables.
 }
 \description{
-  The function takes a specification, consisting of a list of the observed variables
-  in the data. Each observed variable is again represented by a list, specifying the 
-  kinetic model type and reaction or transfer to other observed compartments.
+  The function usually takes several expressions, each assigning a compound name to 
+  a list, specifying the kinetic model type and reaction or transfer to other
+  observed compartments. Instead of specifying several expressions, a list
+  of lists can be given in the speclist argument.
+
+  For the definition of model types and their parameters, the equations given
+  in the FOCUS and NAFTA guidance documents are used.
 }
 \usage{
 mkinmod(..., use_of_ff = "min", speclist = NULL)
@@ -15,10 +19,11 @@ mkinmod(..., use_of_ff = "min", speclist = NULL)
   \item{...}{
     For each observed variable, a list has to be specified as an argument, containing
     at least a component \code{type}, specifying the type of kinetics to use
-    for the variable. Currently, single first order kinetics "SFO" or
+    for the variable. Currently, single first order kinetics "SFO", 
+    indeterminate order rate equation kinetics "IORE", or
     single first order with reversible binding "SFORB" are implemented for all
     variables, while 
-    "FOMC", "IORE", "DFOP" and "HS" can additionally be chosen for the first
+    "FOMC", "DFOP" and "HS" can additionally be chosen for the first
     variable which is assumed to be the source compartment.
     Additionally, each component of the list can include a character vector \code{to},
     specifying names of variables to which a transfer is to be assumed in the
@@ -49,6 +54,17 @@ mkinmod(..., use_of_ff = "min", speclist = NULL)
     \item{coefmat}{ The coefficient matrix, if the system of differential equations can be
       represented by one. }
 }
+\references{
+  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and
+  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+  Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+  \url{http://focus.jrc.ec.europa.eu/dk} 
+
+  NAFTA Technical Working Group on Pesticides (not dated) Guidance for
+  Evaluating and Calculating Degradation Kinetics in Environmental 
+  Media
+}
 \author{
   Johannes Ranke
 }
diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index 97db90e3..7d8979e4 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -65,21 +65,25 @@
 }
 \examples{
   SFO <- mkinmod(degradinol = list(type = "SFO"))
+  # Compare solution types
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
 	      solution_type = "analytical")
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
+	      solution_type = "deSolve")
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
 	      solution_type = "eigen")
 
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 1:20, 
-	      solution_type = "analytical")[20,]
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
-	      atol = 1e-20)[20,]
 
-  # The integration method does not make a lot of difference
+  # Compare integration methods to analytical solution
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
-	      atol = 1e-20, method = "ode45")[20,]
+	      solution_type = "analytical")[21,]
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
-	      atol = 1e-20, method = "rk4")[20,]
+	      method = "lsoda")[21,]
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+	      method = "ode45")[21,]
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+	      method = "rk4")[21,]
+ # rk4 is not as precise here
 
   # The number of output times used to make a lot of difference until the
   # default for atol was adjusted
@@ -87,5 +91,6 @@
 	      seq(0, 20, by = 0.1))[201,]
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 
 	      seq(0, 20, by = 0.01))[2001,]
+
 }
 \keyword{ manip }
-- 
cgit v1.2.1