diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/mkinfit.R | 7 | ||||
| -rw-r--r-- | R/mkinplot.R | 2 | ||||
| -rw-r--r-- | R/mkinpredict.R | 3 |
3 files changed, 7 insertions, 5 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index 3100b30..0215596 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$date <- date()
diff --git a/R/mkinplot.R b/R/mkinplot.R index 7641d26..546c506 100644 --- a/R/mkinplot.R +++ b/R/mkinplot.R @@ -18,7 +18,7 @@ mkinplot <- function(fit, xlab = "Time", ylab = "Observed", xlim = range(fit$dat odeparms <- parms.all[odenames] out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, - solution_type = solution_type, ...) + solution_type = solution_type, atol = fit$atol, rtol = fit$rtol, ...) # Plot the data and model output plot(0, type="n", diff --git a/R/mkinpredict.R b/R/mkinpredict.R index 493c578..5170dc6 100644 --- a/R/mkinpredict.R +++ b/R/mkinpredict.R @@ -18,7 +18,7 @@ # You should have received a copy of the GNU General Public License along with # this program. If not, see <http://www.gnu.org/licenses/> -mkinpredict <- function(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve", map_output = TRUE, atol = 1e-6, ...) { +mkinpredict <- function(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve", map_output = TRUE, atol = 1e-8, rtol = 1e-10, ...) { # Get the names of the state variables in the model mod_vars <- names(mkinmod$diffs) @@ -92,6 +92,7 @@ mkinpredict <- function(mkinmod, odeparms, odeini, outtimes, solution_type = "de func = mkindiff, parms = odeparms, atol = atol, + rtol = rtol, ... ) } |