diff options
Diffstat (limited to 'R/mkinpredict.R')
| -rw-r--r-- | R/mkinpredict.R | 24 |
1 files changed, 20 insertions, 4 deletions
diff --git a/R/mkinpredict.R b/R/mkinpredict.R index 60456fb2..2c865cb7 100644 --- a/R/mkinpredict.R +++ b/R/mkinpredict.R @@ -22,7 +22,7 @@ #' 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 +#' @param method.ode The solution method passed via [mkinpredict] to `deSolve::ode()` in #' 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 @@ -36,7 +36,7 @@ #' the observed variables (default) or for all state variables (if set to #' FALSE). Setting this to FALSE has no effect for analytical solutions, #' as these always return mapped output. -#' @param na_stop Should it be an error if [ode] returns NaN values +#' @param na_stop Should it be an error if `deSolve::ode()` returns NaN values #' @param \dots Further arguments passed to the ode solver in case such a #' solver is used. #' @return A matrix with the numeric solution in wide format @@ -172,6 +172,15 @@ mkinpredict.mkinmod <- function(x, } if (solution_type == "deSolve") { + + # We need to make sure that 0 is included in outtimes, + # even if we do not have observed data for time zero, + # because otherwise the initial values are not applied + # to time zero but to the time of the first observation + # in the data + if (min(outtimes) > 0) outtimes_deSolve <- c(0, outtimes) + else outtimes_deSolve <- outtimes + if (!is.null(x$cf) & use_compiled[1] != FALSE) { if (!is.null(x$symbols) & use_symbols) { @@ -182,7 +191,7 @@ mkinpredict.mkinmod <- function(x, out <- deSolve::lsoda( y = odeini, - times = outtimes, + times = outtimes_deSolve, func = lsoda_func, initfunc = "initpar", dllname = x$dll_info[["name"]], @@ -209,7 +218,7 @@ mkinpredict.mkinmod <- function(x, } out <- deSolve::ode( y = odeini, - times = outtimes, + times = outtimes_deSolve, func = mkindiff, parms = odeparms, method = method.ode, @@ -219,6 +228,13 @@ mkinpredict.mkinmod <- function(x, ... ) } + + # Now we need to remove time zero, in case we did not + # have observations for it + if (min(outtimes) > 0) { + out <- out[-1, ] + } + n_out_na <- sum(is.na(out)) if (n_out_na > 0 & na_stop) { cat("odeini:\n") |