diff options
| -rw-r--r-- | R/mkinmod.R | 9 | ||||
| -rw-r--r-- | inst/unitTests/runit.mkinfit.R | 14 | ||||
| -rw-r--r-- | inst/unitTests/runit.mkinpredict.R | 20 |
3 files changed, 37 insertions, 6 deletions
diff --git a/R/mkinmod.R b/R/mkinmod.R index e73c56c6..3fff0878 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -126,8 +126,8 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL) }
} #}}}
if(spec[[varname]]$type == "FOMC") { # {{{ Add FOMC decline term
- # From p. 53 of the FOCUS kinetics report
- decline_term <- paste("(alpha/beta) * ((time/beta) + 1)^-1 *", box_1)
+ # From p. 53 of the FOCUS kinetics report, without the power function so it works in C
+ decline_term <- paste("(alpha/beta) * 1/((time/beta) + 1) *", box_1)
parms <- c(parms, "alpha", "beta")
} #}}}
if(spec[[varname]]$type == "DFOP") { # {{{ Add DFOP decline term
@@ -295,10 +295,9 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL) 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$type %in% c("SFO", "SFORB"))) == length(spec)) {
+ if (sum(sapply(spec, function(x) x$type %in% c("SFO", "FOMC", "DFOP", "SFORB"))) == length(spec)) {
message("Compiling differential equation model from auto-generated C code...")
- model$compiled <- compile.ode(diffs.C, language = "C", parms = parms)
+ model$compiled <- compile.ode(diffs.C, language = "C", parms = parms, declaration = "double time = *t;")
}
}
# }}}
diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R index 8eefb995..01cbaf00 100644 --- a/inst/unitTests/runit.mkinfit.R +++ b/inst/unitTests/runit.mkinfit.R @@ -1,4 +1,4 @@ -# Copyright (C) 2010-2014 Johannes Ranke
+# Copyright (C) 2010-2015 Johannes Ranke
# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
@@ -112,6 +112,18 @@ test.FOCUS_2006_DFOP <- function() dev.B.DFOP <- abs(round(100 * ((median.B.DFOP - fit.B.DFOP.r)/median.B.DFOP), digits=1))
# about 0.6% deviation for parameter f, the others are <= 0.1%
checkIdentical(dev.B.DFOP < 1, rep(TRUE, length(dev.B.DFOP)))
+
+ # Check the compiled version of possible FOCUS_2006_B
+ if (require(ccSolve)) {
+ checkTrue(!is.null(DFOP$compiled))
+ fit.B.DFOP.compiled <- mkinfit(DFOP, FOCUS_2006_B, solution_type = "deSolve", use_compiled = TRUE, quiet=TRUE)
+
+ fit.B.DFOP.compiled.r <- as.numeric(c(fit.B.DFOP.compiled$bparms.optim,
+ endpoints(fit.B.DFOP)$distimes[c("DT50", "DT90")]))
+ dev.B.DFOP.compiled <- abs(round(100 * ((median.B.DFOP - fit.B.DFOP.compiled.r)/median.B.DFOP), digits=1))
+ # about 0.6% deviation for parameter f, the others are <= 0.1%
+ checkIdentical(dev.B.DFOP.compiled < 1, rep(TRUE, length(dev.B.DFOP)))
+ }
} # }}}
# Test HS model to a relative tolerance of 1% excluding Mathematica values {{{
diff --git a/inst/unitTests/runit.mkinpredict.R b/inst/unitTests/runit.mkinpredict.R index d30bcfab..6635ea1f 100644 --- a/inst/unitTests/runit.mkinpredict.R +++ b/inst/unitTests/runit.mkinpredict.R @@ -34,6 +34,26 @@ test.SFO_solution_types <- function() checkEquals(SFO.analytical, SFO.eigen)
} # }}}
+# Check solution types for FOMC {{{
+test.FOMC_solution_types <- function()
+{
+ ot = seq(0, 100, by = 1)
+ FOMC <- mkinmod(parent = list(type = "FOMC"))
+ FOMC.analytical <- round(subset(mkinpredict(FOMC, c(alpha = 1, beta = 10),
+ c(parent = 100), ot, solution_type = "analytical"), time == 100), digits=5)
+ FOMC.deSolve <- round(subset(mkinpredict(FOMC, c(alpha = 1, beta = 10),
+ c(parent = 100), ot, solution_type = "deSolve"), use_compiled = FALSE, time == 100), digits=5)
+ checkEquals(FOMC.analytical, FOMC.deSolve)
+
+ if (require(ccSolve)) {
+ checkTrue(!is.null(FOMC$compiled))
+ FOMC.deSolve.compiled <- round(subset(mkinpredict(FOMC, c(alpha = 1, beta = 10),
+ c(parent = 100), ot, solution_type = "deSolve"), time == 100), digits=5)
+ checkEquals(FOMC.analytical, FOMC.deSolve.compiled)
+ }
+
+} # }}}
+
# Check model specification and solution types for SFO_SFO {{{
# Relative Tolerance is 0.01%
# Do not use time 0, as eigenvalue based solution does not give 0 at time 0 for metabolites
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