# 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)
} # }}}
