- Some more unit tests

- Some more other tests in test.R
- Adaptation of mkinplot



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@36 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

1 files changed, 75 insertions, 0 deletions

diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R
index 2030f85..e2fc8c3 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: