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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-27 21:52:21 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-27 21:52:21 +0100
commit7a349394413d533d7dab5d18bb29bc761dcd5659 (patch)
tree5817d52007a08405fd3120f32656a813d2422389 /R/mkinmod.R
parenteaf3073bf0aeee812574b32f7e557218c61c6255 (diff)
parent1e3fd1bef2a0ec1c8b73fcfefdd62fd3463bc87c (diff)
Merge branch 'saving_compiled_code'
Diffstat (limited to 'R/mkinmod.R')
-rw-r--r--R/mkinmod.R78
1 files changed, 49 insertions, 29 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")

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