- Document endpoints() function

- Fix unit tests that were broken by introduction of 
  the endpoints function
- Small documentation fixes
- Format output of backtransformed parameters
- Integrate snippet for making static documentation
  using staticdocs by Hadley Wickham



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@41 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

3 files changed, 35 insertions, 2 deletions

diff --git a/man/endpoints.Rd b/man/endpoints.Rd
new file mode 100644
index 00000000..21316cf2
--- /dev/null
+++ b/man/endpoints.Rd
@@ -0,0 +1,33 @@
+\name{endpoints}
+\alias{endpoints}
+\title{
+Function to calculate endpoints for further use from kinetic models fitted with mkinfit
+}
+\description{
+This function calculates DT50 and DT90 values as well as formation fractions from kinetic models
+fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, 
+the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but 
+with the advantage that the SFORB model can also be used for metabolites.
+}
+\usage{
+endpoints(fit, pseudoDT50 = FALSE)
+}
+\arguments{
+  \item{fit}{
+  An object of class \code{\link{mkinfit}}.
+}
+  \item{pseudoDT50}{
+  Should pseudoDT50 values for FOMC, DFOP and SFORB models be reported, as 
+  recommended by the FOCUS group? Currently not implemented.
+}
+}
+\note{
+  The function is used internally by \code{\link{summary.mkinfit}}.
+}
+\value{
+  A list with the components mentioned above.
+}
+\author{
+  Johannes Ranke
+}
+\keyword{ manip }
diff --git a/man/ilr.Rd b/man/ilr.Rd
index 8bf7a728..cedb49ca 100644
--- a/man/ilr.Rd
+++ b/man/ilr.Rd
@@ -38,7 +38,7 @@ ilr(c(10, 1, 0.1))
 ilr(c(3, 3, 3))
 # Almost equal entries give small numbers
 ilr(c(0.3, 0.4, 0.3))
-# Only the ration between the numbers counts, not their sum
+# Only the ratio between the numbers counts, not their sum
 invilr(ilr(c(0.7, 0.29, 0.01)))
 invilr(ilr(2.1 * c(0.7, 0.29, 0.01)))
 # Inverse transformation of larger numbers gives unequal elements
diff --git a/man/schaefer07_complex_case.Rd b/man/schaefer07_complex_case.Rd
index f2f024a2..ed4f6941 100644
--- a/man/schaefer07_complex_case.Rd
+++ b/man/schaefer07_complex_case.Rd
@@ -24,7 +24,7 @@
   }

   The results are a data frame with 14 results for different parameter values

 }

-\source{

+\references{

   Schäfer D, Mikolasch M, Rainbird P and Harvey B (2007). KinGUI: a new kinetic

   software tool for evaluations according to FOCUS degradation kinetics. In: Del

   Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII