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 ++++++++++++++++++
 1 file changed, 18 insertions(+)

(limited to 'man/mkinfit.Rd')

diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 0c5d76a9..839580a1 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?
-- 
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