From 5b28712ad11470293e7ab6746718ab3edcfe966b Mon Sep 17 00:00:00 2001 From: jranke Date: Tue, 3 Jul 2012 15:46:14 +0000 Subject: - 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 --- R/mkinfit.R | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'R/mkinfit.R') 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() -- cgit v1.2.1