diff options
Diffstat (limited to 'R/mkinpredict.R')
| -rw-r--r-- | R/mkinpredict.R | 37 |
1 files changed, 18 insertions, 19 deletions
diff --git a/R/mkinpredict.R b/R/mkinpredict.R index 0dc9cf55..f0d00319 100644 --- a/R/mkinpredict.R +++ b/R/mkinpredict.R @@ -19,18 +19,17 @@ #' @param solution_type The method that should be used for producing the #' predictions. This should generally be "analytical" if there is only one #' observed variable, and usually "deSolve" in the case of several observed -#' variables. The third possibility "eigen" is faster but not applicable to -#' some models e.g. using FOMC for the parent compound. +#' variables. The third possibility "eigen" is fast in comparison to uncompiled +#' ODE models, but not applicable to some models, e.g. using FOMC for the +#' parent compound. #' @param method.ode The solution method passed via [mkinpredict] to [ode]] in -#' case the solution type is "deSolve". The default "lsoda" is performant, but -#' sometimes fails to converge. +#' case the solution type is "deSolve" and we are not using compiled code. +#' When using compiled code, only lsoda is supported. #' @param use_compiled If set to \code{FALSE}, no compiled version of the #' [mkinmod] model is used, even if is present. -#' @param atol Absolute error tolerance, passed to [ode]. Default is 1e-8, -#' lower than in [lsoda]. -#' @param rtol Absolute error tolerance, passed to [ode]. Default is 1e-10, -#' much lower than in [lsoda]. -#' @param maxsteps Maximum number of steps, passed to [ode]. +#' @param atol Absolute error tolerance, passed to the ode solver. +#' @param rtol Absolute error tolerance, passed to the ode solver. +#' @param maxsteps Maximum number of steps, passed to the ode solver. #' @param map_output Boolean to specify if the output should list values for #' the observed variables (default) or for all state variables (if set to #' FALSE). Setting this to FALSE has no effect for analytical solutions, @@ -38,7 +37,6 @@ #' @param na_stop Should it be an error if [ode] returns NaN values #' @param \dots Further arguments passed to the ode solver in case such a #' solver is used. -#' @import deSolve #' @return A matrix with the numeric solution in wide format #' @author Johannes Ranke #' @examples @@ -58,11 +56,11 @@ #' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20, #' solution_type = "analytical")[21,] #' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20, -#' method = "lsoda")[21,] +#' method = "lsoda", use_compiled = FALSE)[21,] #' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20, -#' method = "ode45")[21,] +#' method = "ode45", use_compiled = FALSE)[21,] #' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20, -#' method = "rk4")[21,] +#' method = "rk4", use_compiled = FALSE)[21,] #' # rk4 is not as precise here #' #' # The number of output times used to make a lot of difference until the @@ -116,9 +114,10 @@ mkinpredict.mkinmod <- function(x, outtimes = seq(0, 120, by = 0.1), solution_type = "deSolve", use_compiled = "auto", - method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, maxsteps = 20000, + method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, maxsteps = 20000L, map_output = TRUE, na_stop = TRUE, + call_lsoda = NULL, ...) { @@ -173,20 +172,20 @@ mkinpredict.mkinmod <- function(x, if (solution_type == "deSolve") { if (!is.null(x$cf) & use_compiled[1] != FALSE) { - out <- deSolve::ode( + out <- deSolve::lsoda( y = odeini, times = outtimes, - func = "diffs", + func = mkinmod[["symbols"]], initfunc = "initpar", - dllname = if (is.null(x$dll_info)) inline::getDynLib(x$cf)[["name"]] - else x$dll_info[["name"]], + dllname = x$dll_info[["name"]], parms = odeparms[x$parms], # Order matters when using compiled models - method = method.ode, atol = atol, rtol = rtol, maxsteps = maxsteps, ... ) + + colnames(out) <- c("time", mod_vars) } else { mkindiff <- function(t, state, parms) { |