- Moved the call to mkinerrmin to summary.mkinfit

- The argument to mkinerrmin is now an object of class mkinfit
- Fixed the allocation of parameters to observed variables in mkinerrmin



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@37 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

2 files changed, 13 insertions, 14 deletions

diff --git a/man/mkinerrmin.Rd b/man/mkinerrmin.Rd
index 654115b6..c43d87a1 100644
--- a/man/mkinerrmin.Rd
+++ b/man/mkinerrmin.Rd
@@ -10,30 +10,29 @@ smallest relative error still resulting in passing the chi-squared test
 as defined in the FOCUS kinetics report from 2006.

 }

 \usage{

-mkinerrmin(errdata, n.parms, alpha = 0.05)

+mkinerrmin(fit, alpha = 0.05)

 }

 \arguments{

-  \item{errdata}{

-    A data frame with mean observed values in column named \code{value_mean}

-    and predicted values in column \code{value_pred}.

-}

-  \item{n.parms}{

-    The number of optimized parameters to be taken into account for the data series.

-}

+  \item{fit}{

+    an object of class \code{\link{mkinfit}}.

+  }

   \item{alpha}{

     The confidence level chosen for the chi-squared test.

 }

 }

 \value{

-  A list with the following components:

+  A dataframe with the following components:

   \item{err.min}{The relative error, expressed as a fraction.}

   \item{n.optim}{The number of optimised parameters attributed to the data series.}

-  \item{df}{The number of remaining degrees of freedom for the chi2 error level calculations.

-    Note that mean values are used for the chi2 statistic and therefore every time point with 

-    observed values in the series only counts one time.}

+  \item{df}{The number of remaining degrees of freedom for the chi2 error level

+    calculations.  Note that mean values are used for the chi2 statistic and

+    therefore every time point with observed values in the series only counts

+    one time.}

+  The dataframe has one row for the total dataset and one further row for

+  each observed state variable in the model.

 }

 \details{

-    This function is used internally by \code{\link{mkinfit}}.

+    This function is used internally by \code{\link{summary.mkinfit}}.

 }

 \references{ 

   FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index aaa77e6e..d2931443 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -60,7 +60,7 @@ mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve", map_
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 1:20, solution_type = "analytical")[20,]
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, atol = 1e-20)[20,]
   # The integration method does not make a lot of difference
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, atol = 1e-20, method = "bdf")[20,]
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, atol = 1e-20, method = "ode45")[20,]
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, atol = 1e-20, method = "rk4")[20,]
   # The number of output times does make a lot of difference
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), seq(0, 20, by = 0.1))[201,]