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authorJohannes Ranke <jranke@uni-bremen.de>2015-06-19 17:46:11 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-06-19 17:46:11 +0200
commitec574cff822a1238138c0aa69b3d1459bdc3dfa8 (patch)
treeed35e64ca0a2e51b0974e7fa3efd768aa5bc446a /R/mkinpredict.R
parent6281424beafe531c9891670c3227ab12e9a21990 (diff)
Use odeintr instead of ccSolve for compiling modelsodeintr
Diffstat (limited to 'R/mkinpredict.R')
-rw-r--r--R/mkinpredict.R50
1 files changed, 29 insertions, 21 deletions
diff --git a/R/mkinpredict.R b/R/mkinpredict.R
index 3121f1d7..d91e87df 100644
--- a/R/mkinpredict.R
+++ b/R/mkinpredict.R
@@ -18,11 +18,12 @@
# this program. If not, see <http://www.gnu.org/licenses/>
mkinpredict <- function(mkinmod, odeparms, odeini,
- outtimes, solution_type = "deSolve",
- use_compiled = "auto",
- method.ode = "lsoda", atol = 1e-8, rtol = 1e-10,
+ outtimes, solution_type = c("deSolve", "analytical", "eigen", "odeintr"),
+ method.ode = "lsoda", atol.deSolve = 1e-8, rtol.deSolve = 1e-10,
map_output = TRUE, ...) {
+ solution_type = match.arg(solution_type)
+
# Get the names of the state variables in the model
mod_vars <- names(mkinmod$diffs)
@@ -54,8 +55,8 @@ mkinpredict <- function(mkinmod, odeparms, odeini,
IORE = IORE.solution(outtimes,
evalparse(parent.name),
ifelse(mkinmod$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),
@@ -88,30 +89,26 @@ 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) {
+ mkindiff <- function(t, state, parms) {
- time <- t
- diffs <- vector()
- for (box in names(mkinmod$diffs))
- {
- diffname <- paste("d", box, sep="_")
- diffs[diffname] <- with(as.list(c(time, state, parms)),
- eval(parse(text=mkinmod$diffs[[box]])))
- }
- return(list(c(diffs)))
+ time <- t
+ diffs <- vector()
+ for (box in names(mkinmod$diffs))
+ {
+ diffname <- paste("d", box, sep="_")
+ diffs[diffname] <- with(as.list(c(time, state, parms)),
+ eval(parse(text=mkinmod$diffs[[box]])))
}
- }
+ return(list(c(diffs)))
+ }
out <- ode(
y = odeini,
times = outtimes,
func = mkindiff,
parms = odeparms[mkinmod$parms], # Order matters when using compiled models
method = method.ode,
- atol = atol,
- rtol = rtol,
+ atol = atol.deSolve,
+ rtol = rtol.deSolve,
...
)
if (sum(is.na(out)) > 0) {
@@ -119,6 +116,17 @@ mkinpredict <- function(mkinmod, odeparms, odeini,
"NaN values occurred in output from ode()")
}
}
+ if (solution_type == "odeintr") {
+ if (is.null(mkinmod$e$m)) stop("Method odeintr can not be used as no compiled version of the model is available")
+ odeparms_argstring = ""
+ for (parname in names(odeparms)) {
+ odeparms_argstring = paste0(odeparms_argstring, parname, " = ", odeparms[parname], ", ")
+ }
+ odeparms_argstring = gsub(", $", "", odeparms_argstring)
+ with(as.list(odeparms_argstring), eval(parse(text=paste0("mkinmod$e$m_set_params(", odeparms_argstring, ")"))))
+ out <- mkinmod$e$m_at(init = odeini, times = outtimes)
+ names(out) <- c("time", names(mkinmod$diffs))
+ }
if (map_output) {
# Output transformation for models with unobserved compartments like SFORB
out_mapped <- data.frame(time = out[,"time"])

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