diff options
Diffstat (limited to 'inst/unitTests/runit.mkinfit.R')
| -rw-r--r-- | inst/unitTests/runit.mkinfit.R | 75 |
1 files changed, 75 insertions, 0 deletions
diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R index 2030f852..e2fc8c3f 100644 --- a/inst/unitTests/runit.mkinfit.R +++ b/inst/unitTests/runit.mkinfit.R @@ -222,6 +222,43 @@ test.FOCUS_2006_SFORB <- function() checkIdentical(dev.B.SFORB.2 < 1, rep(TRUE, length(dev.B.SFORB.2)))
} # }}}
+# Test SFO_SFO model with FOCUS_2006_D against Schaefer 2007 paper, tolerance = 1% # {{{
+test.FOCUS_2006_D_SFO_SFO <- function()
+{
+ SFO_SFO.1 <- mkinmod(parent = list(type = "SFO", to = "m1"),
+ m1 = list(type = "SFO"), use_of_ff = "min")
+ SFO_SFO.2 <- mkinmod(parent = list(type = "SFO", to = "m1"),
+ m1 = list(type = "SFO"), use_of_ff = "max")
+
+ fit.1.e <- mkinfit(SFO_SFO.1, FOCUS_2006_D)
+ fit.1.d <- mkinfit(SFO_SFO.1, solution_type = "deSolve", FOCUS_2006_D)
+ #fit.2.e <- mkinfit(SFO_SFO.2, FOCUS_2006_D, plot=TRUE)
+ SFO <- mkinmod(parent = list(type = "SFO"))
+ f.SFO <- mkinfit(SFO, FOCUS_2006_D)
+ #fit.2.e <- mkinfit(SFO_SFO.2, parms.ini = f.SFO$odeparms.final, FOCUS_2006_D)
+ fit.2.d <- mkinfit(SFO_SFO.2, solution_type = "deSolve", FOCUS_2006_D)
+ # Eigenvalue based solution with maximum use of formation fractions only
+ # works correctly with initial parameters very close to final parameters!
+ fit.2.e <- mkinfit(SFO_SFO.2, parms.ini = fit.2.d$odeparms.final, FOCUS_2006_D)
+
+ FOCUS_2006_D_results_schaefer07_means <- c(
+ parent_0 = 99.65, DT50_parent = 7.04, DT50_m1 = 131.34)
+
+ r.1.e <- c(fit.1.e$parms.all[[1]], fit.1.e$distimes[[1]])
+ r.1.d <- c(fit.1.d$parms.all[[1]], fit.1.d$distimes[[1]])
+ r.2.e <- c(fit.2.e$parms.all[[1]], fit.2.e$distimes[[1]])
+ r.2.d <- c(fit.2.d$parms.all[[1]], fit.2.d$distimes[[1]])
+
+ dev.1.e <- 100 * (r.1.e - FOCUS_2006_D_results_schaefer07_means)/r.1.e
+ checkIdentical(as.numeric(abs(dev.1.e)) < 1, rep(TRUE, 3))
+ dev.1.d <- 100 * (r.1.d - FOCUS_2006_D_results_schaefer07_means)/r.1.d
+ checkIdentical(as.numeric(abs(dev.1.d)) < 1, rep(TRUE, 3))
+ dev.2.e <- 100 * (r.2.e - FOCUS_2006_D_results_schaefer07_means)/r.2.e
+ checkIdentical(as.numeric(abs(dev.2.e)) < 1, rep(TRUE, 3))
+ dev.2.d <- 100 * (r.2.d - FOCUS_2006_D_results_schaefer07_means)/r.2.d
+ checkIdentical(as.numeric(abs(dev.2.d)) < 1, rep(TRUE, 3))
+} # }}}
+
# Test eigenvalue based fit to Schaefer 2007 data against solution from conference paper {{{
test.mkinfit.schaefer07_complex_example <- function()
{
@@ -258,4 +295,42 @@ test.mkinfit.schaefer07_complex_example <- function() checkIdentical(r$mkin.deviation < 10, rep(TRUE, length(r$mkin.deviation)))
} # }}}
+# Test deSolve based fit to Schaefer 2007 data against solution from conference paper {{{
+test.mkinfit.schaefer07_complex_example <- function()
+{
+ schaefer07_complex_model <- mkinmod(
+ parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),
+ A1 = list(type = "SFO", to = "A2"),
+ B1 = list(type = "SFO"),
+ C1 = list(type = "SFO"),
+ A2 = list(type = "SFO"))
+
+ # Works fine with n.outtimes = 1000 but takes too much time
+ # fit <- mkinfit(schaefer07_complex_model,
+ # mkin_wide_to_long(schaefer07_complex_case, time = "time"),
+ # n.outtimes = 1000, solution_type = "deSolve")
+ # s <- summary(fit)
+ # r <- schaefer07_complex_results
+ # attach(as.list(fit$parms.all))
+ # k_parent <- sum(k_parent_A1, k_parent_B1, k_parent_C1)
+ # r$mkin <- c(
+ # k_parent,
+ # s$distimes["parent", "DT50"],
+ # s$ff["parent_A1"],
+ # sum(k_A1_sink, k_A1_A2),
+ # s$distimes["A1", "DT50"],
+ # s$ff["parent_B1"],
+ # k_B1_sink,
+ # s$distimes["B1", "DT50"],
+ # s$ff["parent_C1"],
+ # k_C1_sink,
+ # s$distimes["C1", "DT50"],
+ # s$ff["A1_A2"],
+ # k_A2_sink,
+ # s$distimes["A2", "DT50"])
+ # r$means <- (r$KinGUI + r$ModelMaker)/2
+ # r$mkin.deviation <- abs(round(100 * ((r$mkin - r$means)/r$means), digits=1))
+ # checkIdentical(r$mkin.deviation < 10, rep(TRUE, length(r$mkin.deviation)))
+} # }}}
+
# vim: set foldmethod=marker ts=2 sw=2 expandtab:
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