diff options
Diffstat (limited to 'R/mkinfit.R')
| -rw-r--r-- | R/mkinfit.R | 23 |
1 files changed, 11 insertions, 12 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index 5118519a..ce380243 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -26,9 +26,8 @@ mkinfit <- function(mkinmod, observed, state.ini = "auto",
fixed_parms = NULL,
fixed_initials = names(mkinmod$diffs)[-1],
- solution_type = c("auto", "analytical", "eigen", "deSolve"),
+ solution_type = c("auto", "analytical", "eigen", "deSolve", "odeintr"),
method.ode = "lsoda",
- use_compiled = "auto",
method.modFit = c("Port", "Marq", "SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B"),
maxit.modFit = "auto",
control.modFit = list(),
@@ -208,8 +207,7 @@ mkinfit <- function(mkinmod, observed, # Decide if the solution of the model can be based on a simple analytical
# formula, the spectral decomposition of the matrix (fundamental system)
# or a numeric ode solver from the deSolve package
- # Prefer deSolve over eigen if a compiled model is present and use_compiled
- # is not set to FALSE
+ # Prefer odeintr if a compiled model is present
solution_type = match.arg(solution_type)
if (solution_type == "analytical" && length(mkinmod$spec) > 1)
stop("Analytical solution not implemented for models with metabolites.")
@@ -219,8 +217,11 @@ mkinfit <- function(mkinmod, observed, if (length(mkinmod$spec) == 1) {
solution_type = "analytical"
} else {
- if (!is.null(mkinmod$compiled) & use_compiled[1] != FALSE) {
- solution_type = "deSolve"
+ if (!is.null(mkinmod$e$m)) {
+ solution_type = "odeintr"
+ if (!missing(atol) | !missing(rtol)) {
+ message("When fitting with solution type odeintr, atol and rtol can only be set in the call to mkinmod()")
+ }
} else {
if (is.matrix(mkinmod$coefmat)) {
solution_type = "eigen"
@@ -269,9 +270,8 @@ mkinfit <- function(mkinmod, observed, out <- mkinpredict(mkinmod, parms,
odeini, outtimes,
solution_type = solution_type,
- use_compiled = use_compiled,
method.ode = method.ode,
- atol = atol, rtol = rtol, ...)
+ atol.deSolve = atol, rtol.deSolve = rtol, ...)
assign("out_predicted", out, inherits=TRUE)
@@ -289,9 +289,8 @@ mkinfit <- function(mkinmod, observed, out_plot <- mkinpredict(mkinmod, parms,
odeini, outtimes_plot,
solution_type = solution_type,
- use_compiled = use_compiled,
method.ode = method.ode,
- atol = atol, rtol = rtol, ...)
+ atol.deSolve = atol, rtol.deSolve = rtol, ...)
plot(0, type="n",
xlim = range(observed$time), ylim = c(0, max(observed$value, na.rm=TRUE)),
@@ -319,8 +318,8 @@ mkinfit <- function(mkinmod, observed, if (!transform_rates) {
index_k <- grep("^k_", names(lower))
lower[index_k] <- 0
- index_k.iore <- grep("^k.iore_", names(lower))
- lower[index_k.iore] <- 0
+ index_k__iore <- grep("^k__iore_", names(lower))
+ lower[index_k__iore] <- 0
other_rate_parms <- intersect(c("alpha", "beta", "k1", "k2", "tb"), names(lower))
lower[other_rate_parms] <- 0
}
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