diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2015-06-20 01:06:24 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2015-06-20 03:59:56 +0200 |
| commit | 062b9cc1d084e8bb5e552076fc48ade4b3050644 (patch) | |
| tree | bfb8acaf64fbbefbd7423cf6d0cfdb5119120a26 /R/mkinpredict.R | |
| parent | 6281424beafe531c9891670c3227ab12e9a21990 (diff) | |
Low-level generation of compiled models
As it is unclear if and when ccSolve will be published on CRAN,
the generation, compilation and use of the C version of the
system of differential equations was developed for mkin, inspired and
guided by the code from the ccSolve package. Many thanks again to
Karline Soetaert for all of her work on this and other R packages.
Now all model types, including the Hockey-Stick model for the parent
compund and the IORE model for parent and/or metabolites can be compiled.
Diffstat (limited to 'R/mkinpredict.R')
| -rw-r--r-- | R/mkinpredict.R | 43 |
1 files changed, 27 insertions, 16 deletions
diff --git a/R/mkinpredict.R b/R/mkinpredict.R index 3121f1d7..5f11c35a 100644 --- a/R/mkinpredict.R +++ b/R/mkinpredict.R @@ -54,8 +54,8 @@ mkinpredict <- function(mkinmod, odeparms, odeini, IORE = IORE.solution(outtimes, evalparse(parent.name), ifelse(mkinmod$use_of_ff == "min", - evalparse(paste("k.iore", parent.name, "sink", sep="_")), - evalparse(paste("k.iore", parent.name, sep="_"))), + evalparse(paste("k__iore", parent.name, "sink", sep="_")), + evalparse(paste("k__iore", parent.name, sep="_"))), evalparse("N_parent")), DFOP = DFOP.solution(outtimes, evalparse(parent.name), @@ -88,10 +88,21 @@ mkinpredict <- function(mkinmod, odeparms, odeini, names(out) <- c("time", mod_vars) } if (solution_type == "deSolve") { - if (!is.null(mkinmod$compiled) & use_compiled[1] != FALSE) { - mkindiff <- mkinmod$compiled - } else { - mkindiff <- function(t, state, parms) { + if (!is.null(mkinmod$cf) & use_compiled[1] != FALSE) { + out <- ode( + y = odeini, + times = outtimes, + func = "func", + initfunc = "initpar", + dllname = getDynLib(mkinmod$cf)[["name"]], + parms = odeparms[mkinmod$parms], # Order matters when using compiled models + method = method.ode, + atol = atol, + rtol = rtol, + ... + ) + } else { + mkindiff <- function(t, state, parms) { time <- t diffs <- vector() @@ -103,17 +114,17 @@ mkinpredict <- function(mkinmod, odeparms, odeini, } return(list(c(diffs))) } + out <- ode( + y = odeini, + times = outtimes, + func = mkindiff, + parms = odeparms, + method = method.ode, + atol = atol, + rtol = rtol, + ... + ) } - out <- ode( - y = odeini, - times = outtimes, - func = mkindiff, - parms = odeparms[mkinmod$parms], # Order matters when using compiled models - method = method.ode, - atol = atol, - rtol = rtol, - ... - ) if (sum(is.na(out)) > 0) { stop("Differential equations were not integrated for all output times because\n", "NaN values occurred in output from ode()") |