- Add rtol argument in order to increase the precision of deSolve based

  predictions for complex models
- Improve default values for atol and set rtol default to 1e-10



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@49 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

1 files changed, 4 insertions, 3 deletions

diff --git a/R/mkinfit.R b/R/mkinfit.R
index 3100b30f..02155966 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -29,7 +29,7 @@ mkinfit <- function(mkinmod, observed,
   solution_type = "auto",

   plot = FALSE, quiet = FALSE,

   err = NULL, weight = "none", scaleVar = FALSE,

-  atol = 1e-6, n.outtimes = 100,

+  atol = 1e-8, rtol = 1e-10, n.outtimes = 100,

   trace_parms = FALSE,

   ...)

 {

@@ -130,7 +130,7 @@ mkinfit <- function(mkinmod, observed,
     parms <- backtransform_odeparms(odeparms, mod_vars)

 

     # Solve the system with current transformed parameter values

-    out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, ...)

+    out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, atol = atol, rtol = rtol, ...)

 

     assign("out_predicted", out, inherits=TRUE)

 

@@ -146,7 +146,7 @@ mkinfit <- function(mkinmod, observed,
         outtimes_plot = seq(min(observed$time), max(observed$time), length.out=100)

 

         out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot, 

-          solution_type = solution_type, ...)

+          solution_type = solution_type, atol = atol, rtol = rtol, ...)

 

         plot(0, type="n", 

           xlim = range(observed$time), ylim = range(observed$value, na.rm=TRUE),

@@ -198,6 +198,7 @@ mkinfit <- function(mkinmod, observed,
   data$variable <- ordered(data$variable, levels = obs_vars)

   fit$data <- data[order(data$variable, data$time), ]

   fit$atol <- atol

+  fit$rtol <- rtol

   fit$parms.all <- parms.all # Return all backtransformed parameters for summary

   fit$odeparms.final <- parms.all[mkinmod$parms] # Return ode parameters for further fitting

   fit$date <- date()