Merge branch 'master' into compile_odes

Conflicts
(resolved manually, deleting code that I had
integrated into the RUnit tests for testing the
compiled version):
	.gitignore
	DESCRIPTION
	inst/unitTests/runit.mkinerrmin.R
	inst/unitTests/runit.mkinfit.R
	tests/testthat/test_mkinpredict_SFO_SFO.R
	vignettes/FOCUS_L.html

1 files changed, 0 insertions, 79 deletions

diff --git a/inst/unitTests/runit.mkinerrmin.R b/inst/unitTests/runit.mkinerrmin.R
deleted file mode 100644
index f4cceda6..00000000
--- a/inst/unitTests/runit.mkinerrmin.R
+++ /dev/null
@@ -1,79 +0,0 @@
-# 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")
-
-  # Check fitting with default solution method, and the different possibilities
-  fit.1 <- mkinfit(SFO_SFO.1, FOCUS_2006_D)
-  fit.1.e <- mkinfit(SFO_SFO.1, FOCUS_2006_D, solution_type = "eigen")
-  fit.1.d <- mkinfit(SFO_SFO.1, solution_type = "deSolve", use_compiled = FALSE, FOCUS_2006_D)
-  fit.1.dc <- mkinfit(SFO_SFO.1, solution_type = "deSolve", use_compiled = TRUE, FOCUS_2006_D)
-  fit.2 <- mkinfit(SFO_SFO.2, FOCUS_2006_D)
-  fit.2.e <- mkinfit(SFO_SFO.2, FOCUS_2006_D, solution_type = "eigen")
-  fit.2.d <- mkinfit(SFO_SFO.2, solution_type = "deSolve", use_compiled = FALSE, FOCUS_2006_D)
-  fit.2.dc <- mkinfit(SFO_SFO.2, solution_type = "deSolve", use_compiled = TRUE, FOCUS_2006_D)
-
-  FOCUS_2006_D_results_schaefer07_means <- c(
-    parent_0 = 99.65, DT50_parent = 7.04, DT50_m1 = 131.34)
-
-  r.1 <- c(fit.1$bparms.optim[[1]], endpoints(fit.1)$distimes[[1]])
-  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.1.dc <- c(fit.1.dc$bparms.optim[[1]], endpoints(fit.1.dc)$distimes[[1]])
-  r.2 <- c(fit.2$bparms.optim[[1]], endpoints(fit.2)$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]])
-  r.2.dc <- c(fit.2.dc$bparms.optim[[1]], endpoints(fit.2.dc)$distimes[[1]])
-
-  dev.1 <- 100 * (r.1 - FOCUS_2006_D_results_schaefer07_means)/r.1
-  checkIdentical(as.numeric(abs(dev.1)) < 1, rep(TRUE, 3))
-  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.1.dc <- 100 * (r.1.dc - FOCUS_2006_D_results_schaefer07_means)/r.1.dc 
-  checkIdentical(as.numeric(abs(dev.1.dc)) < 1, rep(TRUE, 3))
-  dev.2 <- 100 * (r.2 - FOCUS_2006_D_results_schaefer07_means)/r.2 
-  checkIdentical(as.numeric(abs(dev.2)) < 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))
-  dev.2.dc <- 100 * (r.2.dc - FOCUS_2006_D_results_schaefer07_means)/r.2.dc 
-  checkIdentical(as.numeric(abs(dev.2.dc)) < 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)
-} # }}}
-
-