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-rw-r--r--DESCRIPTION6
-rw-r--r--NAMESPACE3
-rw-r--r--R/mkinmod.R34
-rw-r--r--R/mkinpredict.R22
-rw-r--r--man/mkinfit.Rd5
5 files changed, 56 insertions, 14 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 03976d1e..0eaf6ebf 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: mkin
Type: Package
Title: Routines for Fitting Kinetic Models with One or More State
Variables to Chemical Degradation Data
-Version: 0.9-35
+Version: 0.9-36
Date: 2015-02-20
Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
email = "jranke@uni-bremen.de"),
@@ -13,11 +13,13 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006).
Includes a function for conveniently defining differential equation models,
model solution based on eigenvalues if possible or using numerical solvers
and a choice of the optimisation methods made available by the FME package.
+ If the ccSolve package and a C compiler is available, differential equation
+ models are solved as compiled C functions.
Please note that no warranty is implied for correctness of results or fitness
for a particular purpose.
Depends: minpack.lm, rootSolve
Imports: FME, deSolve
-Suggests: knitr, RUnit
+Suggests: knitr, RUnit, ccSolve
License: GPL
LazyLoad: yes
LazyData: yes
diff --git a/NAMESPACE b/NAMESPACE
index 4774475e..92f0f271 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -9,5 +9,6 @@ import(
FME,
deSolve,
minpack.lm,
- rootSolve
+ rootSolve,
+ ccSolve
)
diff --git a/R/mkinmod.R b/R/mkinmod.R
index d04f811f..37cd02b4 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -36,6 +36,9 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
# differential equations (if supported), parameter names and a mapping from
# model variables to observed variables. If possible, a matrix representation
# of the differential equations is included
+ # Compiling the functions from the C code generated below using the ccSolve package
+ # only works if the implicit assumption about differential equations specified below
+ # is satisfied
parms <- vector()
# }}}
@@ -269,6 +272,37 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
model$coefmat <- m
}#}}}
+ # Create a function compiled from C code if possible #{{{
+ if (require(ccSolve)) {
+ diffs.C <- paste(diffs, collapse = ";\n")
+ diffs.C <- paste0(diffs.C, ";")
+ for (i in seq_along(diffs)) {
+ obs_var <- names(diffs)[i]
+
+ # Replace d_... terms by f[i-1]
+ # First line
+ pattern <- paste0("^d_", obs_var)
+ replacement <- paste0("\nf[", i - 1, "]")
+ diffs.C <- gsub(pattern, replacement, diffs.C)
+ # Other lines
+ pattern <- paste0("\\nd_", obs_var)
+ replacement <- paste0("\nf[", i - 1, "]")
+ diffs.C <- gsub(pattern, replacement, diffs.C)
+
+ # Replace names of observed variables by y[i],
+ # making the implicit assumption that the observed variables only occur after "* "
+ pattern <- paste0("\\* ", obs_var)
+ replacement <- paste0("* y[", i - 1, "]")
+ diffs.C <- gsub(pattern, replacement, diffs.C)
+ }
+ # Unfortunately, the models with time occuring in the diffs do not compile
+ if (sum(sapply(spec, function(x) x$type %in% c("SFO", "SFORB"))) == length(spec)) {
+ message("Compiling differential equation model from auto-generated C code...")
+ model$compiled <- compile.ode(diffs.C, language = "C", parms = parms)
+ }
+ }
+ # }}}
+
class(model) <- "mkinmod"
return(model)
}
diff --git a/R/mkinpredict.R b/R/mkinpredict.R
index da013d50..bed82441 100644
--- a/R/mkinpredict.R
+++ b/R/mkinpredict.R
@@ -87,17 +87,21 @@ mkinpredict <- function(mkinmod, odeparms, odeini,
names(out) <- c("time", mod_vars)
}
if (solution_type == "deSolve") {
- mkindiff <- function(t, state, parms) {
+ if (!is.null(mkinmod$compiled)) {
+ mkindiff <- mkinmod$compiled
+ } else {
+ mkindiff <- function(t, state, parms) {
- time <- t
- diffs <- vector()
- for (box in names(mkinmod$diffs))
- {
- diffname <- paste("d", box, sep="_")
- diffs[diffname] <- with(as.list(c(time, state, parms)),
- eval(parse(text=mkinmod$diffs[[box]])))
+ time <- t
+ diffs <- vector()
+ for (box in names(mkinmod$diffs))
+ {
+ diffname <- paste("d", box, sep="_")
+ diffs[diffname] <- with(as.list(c(time, state, parms)),
+ eval(parse(text=mkinmod$diffs[[box]])))
+ }
+ return(list(c(diffs)))
}
- return(list(c(diffs)))
}
out <- ode(
y = odeini,
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 9c82f5ff..466f587c 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -235,7 +235,8 @@ SFO_SFO <- mkinmod(
parent = list(type = "SFO", to = "m1", sink = TRUE),
m1 = list(type = "SFO"))
# Fit the model to the FOCUS example dataset D using defaults
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D)
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen")
+fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve")
summary(fit)
# Use stepwise fitting, using optimised parameters from parent only fit, FOMC
@@ -258,10 +259,10 @@ SFORB_SFO <- mkinmod(
m1 = list(type = "SFO"))
# Fit the model to the FOCUS example dataset D using defaults
fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D)
+fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve")
# Use starting parameters from parent only SFORB fit (not really needed in this case)
fit.SFORB = mkinfit(SFORB, FOCUS_2006_D)
fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode)
-}
# Weighted fits, including IRLS
SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),

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