diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/mkinfit.R | 4 | ||||
| -rw-r--r-- | R/mkinmod.R | 66 | ||||
| -rw-r--r-- | R/mkinpredict.R | 17 |
3 files changed, 53 insertions, 34 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index a6efc858..e482285d 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -479,6 +479,10 @@ mkinfit <- function(mkinmod, observed, solution_type = "analytical" } else { if (!is.null(mkinmod$cf) & use_compiled[1] != FALSE) { + try_dynlib <- try(inline::getDynLib(mkinmod$cf)[["path"]]) + if (inherits(try_dynlib, "try-error")) { + mkinmod$cf <- inline::readDynLib(mkinmod$cf_name, mkinmod$cf_dir) + } solution_type = "deSolve" } else { if (is.matrix(mkinmod$coefmat)) { diff --git a/R/mkinmod.R b/R/mkinmod.R index 1af72db5..434282fd 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -11,7 +11,6 @@ #' of the system of differential equations is included in the resulting #' mkinmod object in some cases, speeding up the solution. #' -#' If a C compiler is found by [pkgbuild::has_compiler()] and there #' is more than one observed variable in the specification, C code is generated #' for evaluating the differential equations, compiled using #' [inline::cfunction()] and added to the resulting mkinmod object. @@ -34,16 +33,17 @@ #' 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 name A name for the model. Should be a valid R object name. #' @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 cf_dir Directory where CFunc objects should be saved. Specifying +#' 'cf_dir' without specifying a 'name' for the object is an error. #' @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 +90,17 @@ #' 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 full names used for plotting, and write to user defined location #' 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 = "SFOSFO", cf_dir = tempdir()) +#' fit_sfo_sfo <- mkinfit(SFO_SFO.2, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve") #' #' # Show details of creating the C function #' SFO_SFO <- mkinmod( @@ -125,12 +125,18 @@ #' } #' #' @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, cf_dir = NULL) { if (is.null(speclist)) spec <- list(...) else spec <- speclist obs_vars <- names(spec) + if (!is.null(cf_dir)) { + if (!dir.exists(cf_dir)) stop(cf_dir, " does not exist") + if (is.null(name)) stop("You must give a name if you want to use 'cf_dir'") + } + # 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") @@ -372,7 +378,7 @@ 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 +438,27 @@ 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) + cf <- try(inline::cfunction(derivs_sig, derivs_code, + otherdefs = initpar_code, + verbose = verbose, + 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$cf <- cf + if (is.null(cf_dir)) { + model$cf <- cf + if (!quiet) message("Temporary DLL for differentials generated and loaded") + } else { + cf_file <- inline::writeDynLib(cf, name, cf_dir) + model$cf <- inline::readDynLib(name, cf_dir) + model$cf_name <- name + model$cf_dir <- cf_dir + fileDLL <- inline::getDynLib(model$cf)[["path"]] + if (!quiet) { + message("CFunc object written to ", cf_file) + message("DLL written to ", fileDLL) + } + } } } # }}} @@ -459,14 +477,6 @@ 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..a294a114 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 +169,18 @@ mkinpredict.mkinmod <- function(x, if (solution_type == "deSolve") { if (!is.null(x$cf) & use_compiled[1] != FALSE) { - out <- ode( + DLL <- try(inline::getDynLib(x$cf)) + if (inherits(DLL, "try-error")) { + x$cf <- inline::readDynLib(x$cf_name, x$cf_dir) + } + cf_env <- environment(x$cf) + + out <- deSolve::ode( y = odeini, times = outtimes, - func = "func", + func = cf_env$name, initfunc = "initpar", - dllname = getDynLib(x$cf)[["name"]], + dllname = cf_env$f, parms = odeparms[x$parms], # Order matters when using compiled models method = method.ode, atol = atol, @@ -195,7 +200,7 @@ mkinpredict.mkinmod <- function(x, } return(list(c(diffs))) } - out <- ode( + out <- deSolve::ode( y = odeini, times = outtimes, func = mkindiff, |