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-rw-r--r--man/transform_odeparms.Rd50
1 files changed, 41 insertions, 9 deletions
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
index c52fb4f1..ea0b5024 100644
--- a/man/transform_odeparms.Rd
+++ b/man/transform_odeparms.Rd
@@ -11,10 +11,15 @@
simple log transformation is used. For compositional parameters, such as
the formations fractions that should always sum up to 1 and can not be
negative, the \code{\link{ilr}} transformation is used.
+
+ The transformation of sets of formation fractions is fragile, as it supposes
+ the same ordering of the components in forward and backward transformation.
+ This is no problem for the internal use in \code{\link{mkinfit}}.
}
\usage{
-transform_odeparms(parms, mod_vars, transform_rates = TRUE, transform_fractions = TRUE)
-backtransform_odeparms(transparms, mod_vars,
+transform_odeparms(parms, mkinmod,
+ transform_rates = TRUE, transform_fractions = TRUE)
+backtransform_odeparms(transparms, mkinmod,
transform_rates = TRUE, transform_fractions = TRUE)
}
\arguments{
@@ -24,9 +29,11 @@ backtransform_odeparms(transparms, mod_vars,
\item{transparms}{
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.
+ \item{mkinmod}{
+ The kinetic model of class \code{\link{mkinmod}}, containing the names of
+ the model variables that are needed for grouping the formation fractions
+ before \code{\link{ilr}} transformation, the parameter names and
+ the information if the pathway to sink is included in the model.
}
\item{transform_rates}{
Boolean specifying if kinetic rate constants should be transformed in the
@@ -59,11 +66,36 @@ SFO_SFO <- mkinmod(
m1 = list(type = "SFO"))
# Fit the model to the FOCUS example dataset D using defaults
fit <- mkinfit(SFO_SFO, FOCUS_2006_D)
+fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)
summary(fit, data=FALSE) # See transformed and backtransformed parameters
+summary(fit.2, data=FALSE)
initials <- fit$start$value
-transformed <- fit$start$transformed
-names(initials) <- names(transformed) <- rownames(fit$start)
-transform_odeparms(initials, c("parent", "m1"))
-backtransform_odeparms(transformed, c("parent", "m1"))
+names(initials) <- rownames(fit$start)
+transformed <- fit$start_transformed$value
+names(transformed) <- rownames(fit$start_transformed)
+transform_odeparms(initials, SFO_SFO)
+backtransform_odeparms(transformed, SFO_SFO)
+
+# The case of formation fractions
+SFO_SFO.ff <- mkinmod(
+ parent = list(type = "SFO", to = "m1", sink = TRUE),
+ m1 = list(type = "SFO"),
+ use_of_ff = "max")
+
+fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D)
+summary(fit.ff, data = FALSE)
+initials <- c("f_parent_to_m1" = 0.5)
+transformed <- transform_odeparms(initials, SFO_SFO.ff)
+backtransform_odeparms(transformed, SFO_SFO.ff)
+
+# And without sink
+SFO_SFO.ff.2 <- mkinmod(
+ parent = list(type = "SFO", to = "m1", sink = FALSE),
+ m1 = list(type = "SFO"),
+ use_of_ff = "max")
+
+
+fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D)
+summary(fit.ff.2, data = FALSE)
}
\keyword{ manip }

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