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authorJohannes Ranke <jranke@uni-bremen.de>2014-04-22 19:08:09 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2014-04-22 19:08:09 +0200
commita2f772990127891f9596b79771832bc23777a89a (patch)
tree1580440d543727db6a0dbd9005936836a0e49746 /man
parentadcbcf246acf92c50c339a6605608a5dd9c580ff (diff)
Possibility to fit without parameter transformation
Diffstat (limited to 'man')
-rw-r--r--man/mkinfit.Rd18
-rw-r--r--man/transform_odeparms.Rd35
2 files changed, 44 insertions, 9 deletions
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?
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
index 999beaaf..e251cf62 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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