diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/mkinfit.R | 14 | ||||
| -rw-r--r-- | R/mkinmod.R | 2 | ||||
| -rw-r--r-- | R/mkinpredict.R | 13 | ||||
| -rw-r--r-- | R/plot.mixed.mmkin.R | 10 | ||||
| -rw-r--r-- | R/plot.mkinfit.R | 5 | ||||
| -rw-r--r-- | R/saem.R | 8 |
6 files changed, 36 insertions, 16 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index b97bc7e2..c851fddb 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -501,10 +501,15 @@ mkinfit <- function(mkinmod, observed, } # Get native symbol before iterations info for speed + use_symbols = FALSE if (solution_type == "deSolve" & use_compiled[1] != FALSE) { - mkinmod[["symbols"]] <- deSolve::checkDLL(dllname = mkinmod$dll_info[["name"]], - func = "diffs", initfunc = "initpar", - jacfunc = NULL, nout = 0, outnames = NULL) + mkinmod[["symbols"]] <- try( + deSolve::checkDLL(dllname = mkinmod$dll_info[["name"]], + func = "diffs", initfunc = "initpar", + jacfunc = NULL, nout = 0, outnames = NULL)) + if (!inherits(mkinmod[["symbols"]], "try-error")) { + use_symbols = TRUE + } } # Get the error model and the algorithm for fitting @@ -616,8 +621,9 @@ mkinfit <- function(mkinmod, observed, odeini, outtimes, solution_type = solution_type, use_compiled = use_compiled, + use_symbols = use_symbols, method.ode = method.ode, - atol = atol, rtol = rtol, + atol = atol, rtol = rtol, ...) observed_index <- cbind(as.character(observed$time), as.character(observed$name)) diff --git a/R/mkinmod.R b/R/mkinmod.R index 29542b71..2f930adb 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -464,11 +464,11 @@ mkinmod <- function(..., use_of_ff = "max", name = NULL, silent = TRUE) if (!inherits(model$cf, "try-error")) { + if (!quiet) message("Temporary DLL for differentials generated and loaded") if (!is.null(dll_dir)) { model$dll_info <- inline::moveDLL(model$cf, name, dll_dir, unload = unload, overwrite = overwrite, verbose = !quiet) } - if (!quiet) message("Temporary DLL for differentials generated and loaded") model$dll_info <- inline::getDynLib(model$cf) } } diff --git a/R/mkinpredict.R b/R/mkinpredict.R index 957d5793..60456fb2 100644 --- a/R/mkinpredict.R +++ b/R/mkinpredict.R @@ -27,6 +27,8 @@ #' When using compiled code, only lsoda is supported. #' @param use_compiled If set to \code{FALSE}, no compiled version of the #' [mkinmod] model is used, even if is present. +#' @param use_symbols If set to \code{TRUE} (default), symbol info present in +#' the [mkinmod] object is used if available for accessing compiled code #' @param atol Absolute error tolerance, passed to the ode solver. #' @param rtol Absolute error tolerance, passed to the ode solver. #' @param maxsteps Maximum number of steps, passed to the ode solver. @@ -114,6 +116,7 @@ mkinpredict.mkinmod <- function(x, outtimes = seq(0, 120, by = 0.1), solution_type = "deSolve", use_compiled = "auto", + use_symbols = FALSE, method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, maxsteps = 20000L, map_output = TRUE, na_stop = TRUE, @@ -169,12 +172,18 @@ mkinpredict.mkinmod <- function(x, } if (solution_type == "deSolve") { - if (!is.null(x$cf) & !is.null(x$symbols) & use_compiled[1] != FALSE) { + if (!is.null(x$cf) & use_compiled[1] != FALSE) { + + if (!is.null(x$symbols) & use_symbols) { + lsoda_func <- x$symbols + } else { + lsoda_func <- "diffs" + } out <- deSolve::lsoda( y = odeini, times = outtimes, - func = x$symbols, + func = lsoda_func, initfunc = "initpar", dllname = x$dll_info[["name"]], parms = odeparms[x$parms], # Order matters when using compiled models diff --git a/R/plot.mixed.mmkin.R b/R/plot.mixed.mmkin.R index 466e55fc..d6c3d0de 100644 --- a/R/plot.mixed.mmkin.R +++ b/R/plot.mixed.mmkin.R @@ -166,10 +166,12 @@ plot.mixed.mmkin <- function(x, } } - # Make sure degparms_pop is a matrix, columns corresponding to population curve(s) - if (is.null(dim(degparms_pop))) { - degparms_pop <- matrix(degparms_pop, ncol = 1, - dimnames = list(names(degparms_pop), "Population")) + if (pop_curves) { + # Make sure degparms_pop is a matrix, columns corresponding to population curve(s) + if (is.null(dim(degparms_pop))) { + degparms_pop <- matrix(degparms_pop, ncol = 1, + dimnames = list(names(degparms_pop), "Population")) + } } degparms_fixed <- fit_1$fixed$value diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index 9606507a..9f19213a 100644 --- a/R/plot.mkinfit.R +++ b/R/plot.mkinfit.R @@ -146,9 +146,8 @@ plot.mkinfit <- function(x, fit = x, func = "diffs", initfunc = "initpar", jacfunc = NULL, nout = 0, outnames = NULL) } - out <- try(mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, - solution_type = solution_type, atol = fit$atol, rtol = fit$rtol), - silent = TRUE) + out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, + solution_type = solution_type, atol = fit$atol, rtol = fit$rtol) out <- as.data.frame(out) @@ -583,11 +583,15 @@ saemix_model <- function(object, solution_type = "auto", transform_fractions <- object[[1]]$transform_fractions # Get native symbol info for speed + use_symbols = FALSE if (solution_type == "deSolve" & !is.null(mkin_model$cf)) { - mkin_model$symbols <- deSolve::checkDLL( + mkin_model$symbols <- try(deSolve::checkDLL( dllname = mkin_model$dll_info[["name"]], func = "diffs", initfunc = "initpar", - jacfunc = NULL, nout = 0, outnames = NULL) + jacfunc = NULL, nout = 0, outnames = NULL)) + if (!inherits(mkin_model$symbols, "try-error")) { + use_symbols = TRUE + } } # Define the model function |