Merge branch 'master' into iore

2 files changed, 63 insertions, 37 deletions

diff --git a/inst/unitTests/runit.mkinerrmin.R b/inst/unitTests/runit.mkinerrmin.R
new file mode 100644
index 00000000..56a33ff9
--- /dev/null
+++ b/inst/unitTests/runit.mkinerrmin.R
@@ -0,0 +1,62 @@
+# Test SFO_SFO model with FOCUS_2006_D against Schaefer 2007 paper, tolerance = 1% # {{{
+# and check chi2 error values against values obtained with mkin 0.33
+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)
+  fit.2.d <- mkinfit(SFO_SFO.2, solution_type = "deSolve", 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$bparms.optim[[1]], endpoints(fit.1.e)$distimes[[1]])
+  r.1.d <- c(fit.1.d$bparms.optim[[1]], endpoints(fit.1.d)$distimes[[1]])
+  r.2.e <- c(fit.2.e$bparms.optim[[1]], endpoints(fit.2.e)$distimes[[1]])
+  r.2.d <- c(fit.2.d$bparms.optim[[1]], endpoints(fit.2.d)$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))
+
+  round(mkinerrmin(fit.2.e), 4)
+  round(mkinerrmin(fit.2.d), 4)
+
+  errmin.FOCUS_2006_D_rounded = data.frame(
+    err.min = c(0.0640, 0.0646, 0.0469),
+    n.optim = c(4, 2, 2),
+    df = c(15, 7, 8), 
+    row.names = c("All data", "parent", "m1"))
+  checkEqualsNumeric(round(mkinerrmin(fit.2.e), 4),
+                     errmin.FOCUS_2006_D_rounded)
+} # }}}
+
+# Test SFO_SFO model with FOCUS_2006_E against values obtained with mkin 0.33 {{{
+test.FOCUS_2006_E_SFO_SFO <- function()
+{
+  SFO_SFO.2 <- mkinmod(parent = list(type = "SFO", to = "m1"),
+         m1 = list(type = "SFO"), use_of_ff = "max")
+
+  fit.2.e <- mkinfit(SFO_SFO.2, FOCUS_2006_E)
+
+  round(mkinerrmin(fit.2.e), 4)
+  errmin.FOCUS_2006_E_rounded = data.frame(
+    err.min = c(0.1544, 0.1659, 0.1095),
+    n.optim = c(4, 2, 2),
+    df = c(13, 7, 6),
+    row.names = c("All data", "parent", "m1"))
+  checkEqualsNumeric(round(mkinerrmin(fit.2.e), 4),
+                     errmin.FOCUS_2006_E_rounded)
+} # }}}
+
+
diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R
index fdbc86e0..8eefb995 100644
--- a/inst/unitTests/runit.mkinfit.R
+++ b/inst/unitTests/runit.mkinfit.R
@@ -1,6 +1,4 @@
-# $Id: runit.mkinfit.R 68 2010-09-09 22:40:04Z jranke $

-

-# Copyright (C) 2010-2013 Johannes Ranke

+# Copyright (C) 2010-2014 Johannes Ranke

 # Contact: jranke@uni-bremen.de

 

 # This file is part of the R package mkin

@@ -189,40 +187,6 @@ 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)

-  SFO <- mkinmod(parent = list(type = "SFO"))

-  f.SFO <- mkinfit(SFO, FOCUS_2006_D)

-  fit.2.d <- mkinfit(SFO_SFO.2, solution_type = "deSolve", FOCUS_2006_D)

-  fit.2.e <- mkinfit(SFO_SFO.2, 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$bparms.optim[[1]], endpoints(fit.1.e)$distimes[[1]])

-  r.1.d <- c(fit.1.d$bparms.optim[[1]], endpoints(fit.1.d)$distimes[[1]])

-  r.2.e <- c(fit.2.e$bparms.optim[[1]], endpoints(fit.2.e)$distimes[[1]])

-  r.2.d <- c(fit.2.d$bparms.optim[[1]], endpoints(fit.2.d)$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()

 {