diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/mkinmod.R | 78 | ||||
| -rw-r--r-- | R/mkinpredict.R | 12 |
2 files changed, 55 insertions, 35 deletions
diff --git a/R/mkinmod.R b/R/mkinmod.R index 1af72db5..a7353e81 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -34,16 +34,23 @@ #' model equations and, if applicable, the coefficient matrix. If "max", #' formation fractions are always used (default). If "min", a minimum use of #' formation fractions is made, i.e. each pathway to a metabolite has its -#' own rate constant. +#' own rate constant. #' @param speclist The specification of the observed variables and their #' submodel types and pathways can be given as a single list using this #' argument. Default is NULL. #' @param quiet Should messages be suppressed? #' @param verbose If \code{TRUE}, passed to [inline::cfunction()] if #' applicable to give detailed information about the C function being built. +#' @param name A name for the model. Should be a valid R object name. +#' @param dll_dir Directory where an DLL object, if generated internally by +#' [inline::cfunction()], should be saved. The DLL will only be stored in a +#' permanent location for use in future sessions, if 'dll_dir' and 'name' +#' are specified. +#' @param unload If a DLL from the target location in 'dll_dir' is already +#' loaded, should that be unloaded first? +#' @param overwrite If a file exists at the target DLL location in 'dll_dir', +#' should this be overwritten? #' @importFrom methods signature -#' @importFrom pkgbuild has_compiler -#' @importFrom inline cfunction #' @return A list of class \code{mkinmod} for use with [mkinfit()], #' containing, among others, #' \item{diffs}{ @@ -90,17 +97,25 @@ #' SFO_SFO <- mkinmod( #' parent = mkinsub("SFO", "m1"), #' m1 = mkinsub("SFO")) +#' print(SFO_SFO) #' #' \dontrun{ -#' # Now supplying full names used for plotting +#' fit_sfo_sfo <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve") +#' +#' # Now supplying compound names used for plotting, and write to user defined location +#' # We need to choose a path outside the session tempdir because this gets removed +#' DLL_dir <- "~/.local/share/mkin" +#' if (!dir.exists(DLL_dir)) dir.create(DLL_dir) #' SFO_SFO.2 <- mkinmod( #' parent = mkinsub("SFO", "m1", full_name = "Test compound"), -#' m1 = mkinsub("SFO", full_name = "Metabolite M1")) -#' -#' # The above model used to be specified like this, before the advent of mkinsub() -#' SFO_SFO <- mkinmod( -#' parent = list(type = "SFO", to = "m1"), -#' m1 = list(type = "SFO")) +#' m1 = mkinsub("SFO", full_name = "Metabolite M1"), +#' name = "SFO_SFO", dll_dir = DLL_dir, unload = TRUE, overwrite = TRUE) +#' # Now we can save the model and restore it in a new session +#' saveRDS(SFO_SFO.2, file = "~/SFO_SFO.rds") +#' # Terminate the R session here if you would like to check, and then do +#' library(mkin) +#' SFO_SFO.3 <- readRDS("~/SFO_SFO.rds") +#' fit_sfo_sfo <- mkinfit(SFO_SFO.3, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve") #' #' # Show details of creating the C function #' SFO_SFO <- mkinmod( @@ -125,12 +140,20 @@ #' } #' #' @export mkinmod -mkinmod <- function(..., use_of_ff = "max", speclist = NULL, quiet = FALSE, verbose = FALSE) +mkinmod <- function(..., use_of_ff = "max", name = NULL, + speclist = NULL, quiet = FALSE, verbose = FALSE, dll_dir = NULL, + unload = FALSE, overwrite = FALSE) { if (is.null(speclist)) spec <- list(...) else spec <- speclist obs_vars <- names(spec) + save_msg <- "You need to specify both 'name' and 'dll_dir' to save a model DLL" + if (!is.null(dll_dir)) { + if (!dir.exists(dll_dir)) stop(dll_dir, " does not exist") + if (is.null(name)) stop(save_msg) + } + # Check if any of the names of the observed variables contains any other for (obs_var in obs_vars) { if (length(grep(obs_var, obs_vars)) > 1) stop("Sorry, variable names can not contain each other") @@ -304,7 +327,7 @@ mkinmod <- function(..., use_of_ff = "max", speclist = NULL, quiet = FALSE, verb } #}}} } #}}} - model <- list(diffs = diffs, parms = parms, map = map, spec = spec, use_of_ff = use_of_ff) + model <- list(diffs = diffs, parms = parms, map = map, spec = spec, use_of_ff = use_of_ff, name = name) # Create coefficient matrix if possible #{{{ if (mat) { @@ -372,7 +395,7 @@ mkinmod <- function(..., use_of_ff = "max", speclist = NULL, quiet = FALSE, verb # Try to create a function compiled from C code if there is more than one observed variable {{{ # and a compiler is available - if (length(obs_vars) > 1 & has_compiler()) { + if (length(obs_vars) > 1 & pkgbuild::has_compiler()) { # Translate the R code for the derivatives to C code diffs.C <- paste(diffs, collapse = ";\n") @@ -432,15 +455,20 @@ mkinmod <- function(..., use_of_ff = "max", speclist = NULL, quiet = FALSE, verb "}\n\n") # Try to build a shared library - cf <- try(cfunction(list(func = derivs_sig), derivs_code, - otherdefs = initpar_code, - verbose = verbose, - convention = ".C", language = "C"), - silent = TRUE) + model$cf <- try(inline::cfunction(derivs_sig, derivs_code, + otherdefs = initpar_code, + verbose = verbose, name = "diffs", + convention = ".C", language = "C"), + silent = TRUE) - if (!inherits(cf, "try-error")) { - if (!quiet) message("Successfully compiled differential equation model from auto-generated C code.") - model$cf <- cf + if (!inherits(model$cf, "try-error")) { + if (is.null(dll_dir)) { + if (!quiet) message("Temporary DLL for differentials generated and loaded") + dll_info <- inline::getDynLib(model$cf) + } else { + dll_info <- inline::moveDLL(model$cf, name, dll_dir, + unload = unload, overwrite = overwrite, verbose = !quiet) + } } } # }}} @@ -459,14 +487,6 @@ mkinmod <- function(..., use_of_ff = "max", speclist = NULL, quiet = FALSE, verb #' #' @rdname mkinmod #' @param x An \code{\link{mkinmod}} object. -#' @examples -#' -#' m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"), -#' M1 = list(type = "SFO", to = "M2"), -#' M2 = list(type = "SFO"), use_of_ff = "max") -#' -#' print(m_synth_SFO_lin) -#' #' @export print.mkinmod <- function(x, ...) { cat("<mkinmod> model generated with\n") diff --git a/R/mkinpredict.R b/R/mkinpredict.R index 7222e247..277c3604 100644 --- a/R/mkinpredict.R +++ b/R/mkinpredict.R @@ -38,7 +38,6 @@ #' @param \dots Further arguments passed to the ode solver in case such a #' solver is used. #' @import deSolve -#' @importFrom inline getDynLib #' @return A matrix with the numeric solution in wide format #' @author Johannes Ranke #' @examples @@ -117,7 +116,7 @@ mkinpredict.mkinmod <- function(x, solution_type = "deSolve", use_compiled = "auto", method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, - map_output = TRUE, + map_output = TRUE, na_stop = TRUE, ...) { @@ -170,12 +169,13 @@ mkinpredict.mkinmod <- function(x, if (solution_type == "deSolve") { if (!is.null(x$cf) & use_compiled[1] != FALSE) { - out <- ode( + + out <- deSolve::ode( y = odeini, times = outtimes, - func = "func", + func = "diffs", initfunc = "initpar", - dllname = getDynLib(x$cf)[["name"]], + dllname = inline::getDynLib(x$cf)[["name"]], parms = odeparms[x$parms], # Order matters when using compiled models method = method.ode, atol = atol, @@ -195,7 +195,7 @@ mkinpredict.mkinmod <- function(x, } return(list(c(diffs))) } - out <- ode( + out <- deSolve::ode( y = odeini, times = outtimes, func = mkindiff, |