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authorJohannes Ranke <jranke@uni-bremen.de>2015-05-15 13:55:19 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-05-15 13:55:19 +0200
commit6c65cba39dbca98caf3f8e69552b3454ec1721fc (patch)
tree00252649aeccfdd13e723054c22203006cab10c6 /inst/unitTests/runit.mkinerrmin.R
parenta26b44d15c11ebb41083fc2efab0cc91a027b55b (diff)
parent89cd81cf47c9f05831e854d5185b5cc599745db4 (diff)
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
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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")
-
- # 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)
-} # }}}
-
-

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