From a2f772990127891f9596b79771832bc23777a89a Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 22 Apr 2014 19:08:09 +0200
Subject: Possibility to fit without parameter transformation

---
 man/mkinfit.Rd            | 18 ++++++++++++++++++
 man/transform_odeparms.Rd | 35 ++++++++++++++++++++++++++---------
 2 files changed, 44 insertions(+), 9 deletions(-)

(limited to 'man')

diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 0c5d76a..839580a 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -23,6 +23,8 @@ mkinfit(mkinmod, observed,
   method.ode = "lsoda",
   method.modFit = "Marq",
   control.modFit = list(),
+  transform_rates = TRUE,
+  transform_fractions = TRUE,
   plot = FALSE, quiet = FALSE, err = NULL, weight = "none", 
   scaleVar = FALSE, 
   atol = 1e-8, rtol = 1e-10, n.outtimes = 100, 
@@ -102,6 +104,22 @@ mkinfit(mkinmod, observed,
     Additional arguments passed to the optimisation method used by
     \code{\link{modFit}}.
   }
+  \item{transform_rates}{
+    Boolean specifying if kinetic rate constants should be transformed in the
+    model specification used in the fitting for better compliance with the
+    assumption of normal distribution of the estimator. If TRUE, also 
+    alpha and beta parameters of the FOMC model are log-transformed, as well 
+    as k1 and k2 rate constants for the DFOP and HS models.
+  }
+  \item{transform_fractions}{
+    Boolean specifying if formation fractions constants should be transformed in the
+    model specification used in the fitting for better compliance with the
+    assumption of normal distribution of the estimator. The default (TRUE) is 
+    to do transformations. The g parameter of the DFOP and HS models are also 
+    transformed, as they can also be seen as compositional data. The
+    transformation used for these transformations is the \code{\link{ilr}}
+    transformation.
+  }
   \item{plot}{
     Should the observed values and the numerical solutions be plotted at each
     stage of the optimisation?
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
index 999beaa..e251cf6 100644
--- a/man/transform_odeparms.Rd
+++ b/man/transform_odeparms.Rd
@@ -13,20 +13,37 @@
   negative, the \code{\link{ilr}} transformation is used.
 }
 \usage{
-transform_odeparms(parms, mod_vars)
-backtransform_odeparms(transparms, mod_vars)
+transform_odeparms(parms, mod_vars, transform_rates = TRUE, transform_fractions = TRUE)
+backtransform_odeparms(transparms, mod_vars, 
+                       transform_rates = TRUE, transform_fractions = TRUE)
 }
 \arguments{
   \item{parms}{
-  Parameters of kinetic models as used in the differential equations.
-}
+    Parameters of kinetic models as used in the differential equations.
+  }
   \item{transparms}{
-  Transformed parameters of kinetic models as used in the fitting procedure.
-}
+    Transformed parameters of kinetic models as used in the fitting procedure.
+  }
   \item{mod_vars}{
-  Names of the state variables in the kinetic model. These are used for 
-  grouping the formation fractions before \code{\link{ilr}} transformation.  
-}
+    Names of the state variables in the kinetic model. These are used for 
+    grouping the formation fractions before \code{\link{ilr}} transformation.  
+  }
+  \item{transform_rates}{
+    Boolean specifying if kinetic rate constants should be transformed in the
+    model specification used in the fitting for better compliance with the
+    assumption of normal distribution of the estimator. If TRUE, also 
+    alpha and beta parameters of the FOMC model are log-transformed, as well 
+    as k1 and k2 rate constants for the DFOP and HS models.
+  }
+  \item{transform_fractions}{
+    Boolean specifying if formation fractions constants should be transformed in the
+    model specification used in the fitting for better compliance with the
+    assumption of normal distribution of the estimator. The default (TRUE) is 
+    to do transformations. The g parameter of the DFOP and HS models are also 
+    transformed, as they can also be seen as compositional data. The
+    transformation used for these transformations is the \code{\link{ilr}}
+    transformation.
+  }
 }
 \value{
   A vector of transformed or backtransformed parameters with the same names
-- 
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