Merge branch 'master' into iore

1 files changed, 62 insertions, 0 deletions

diff --git a/inst/unitTests/runit.mkinerrmin.R b/inst/unitTests/runit.mkinerrmin.R
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+++ b/inst/unitTests/runit.mkinerrmin.R
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+# 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)
+} # }}}
+
+