From a7e6b9f9a0ba46f84929603296d3dd4a0cbe4787 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 26 Jun 2014 11:36:02 +0200 Subject: Calculate additional DT50 values for non-SFO models --- inst/unitTests/runit.mkinfit.R | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) (limited to 'inst') diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R index 9a6bd722..61a0b303 100644 --- a/inst/unitTests/runit.mkinfit.R +++ b/inst/unitTests/runit.mkinfit.R @@ -66,7 +66,7 @@ test.FOCUS_2006_FOMC <- function() median.A.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "A", c(M0, alpha, beta, DT50, DT90)), "median")) - fit.A.FOMC.r <- as.numeric(c(fit.A.FOMC$bparms.optim, endpoints(fit.A.FOMC)$distimes)) + fit.A.FOMC.r <- as.numeric(c(fit.A.FOMC$bparms.optim, endpoints(fit.A.FOMC)$distimes[c("DT50", "DT90")])) dev.A.FOMC <- abs(round(100 * ((median.A.FOMC - fit.A.FOMC.r)/median.A.FOMC), digits=1)) dev.A.FOMC <- dev.A.FOMC[c(1, 4, 5)] checkIdentical(dev.A.FOMC < 1, rep(TRUE, length(dev.A.FOMC))) @@ -77,7 +77,7 @@ test.FOCUS_2006_FOMC <- function() median.B.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "B", c(M0, alpha, beta, DT50, DT90)), "median")) - fit.B.FOMC.r <- as.numeric(c(fit.B.FOMC$bparms.optim, endpoints(fit.B.FOMC)$distimes)) + fit.B.FOMC.r <- as.numeric(c(fit.B.FOMC$bparms.optim, endpoints(fit.B.FOMC)$distimes[c("DT50", "DT90")])) dev.B.FOMC <- abs(round(100 * ((median.B.FOMC - fit.B.FOMC.r)/median.B.FOMC), digits=1)) dev.B.FOMC <- dev.B.FOMC[c(1, 4, 5)] checkIdentical(dev.B.FOMC < 1, rep(TRUE, length(dev.B.FOMC))) @@ -88,7 +88,7 @@ test.FOCUS_2006_FOMC <- function() median.C.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "C", c(M0, alpha, beta, DT50, DT90)), "median")) - fit.C.FOMC.r <- as.numeric(c(fit.C.FOMC$bparms.optim, endpoints(fit.C.FOMC)$distimes)) + fit.C.FOMC.r <- as.numeric(c(fit.C.FOMC$bparms.optim, endpoints(fit.C.FOMC)$distimes[c("DT50", "DT90")])) dev.C.FOMC <- abs(round(100 * ((median.C.FOMC - fit.C.FOMC.r)/median.C.FOMC), digits=1)) dev.C.FOMC <- dev.C.FOMC[c(1, 4, 5)] checkIdentical(dev.C.FOMC < 1, rep(TRUE, length(dev.C.FOMC))) @@ -105,7 +105,7 @@ test.FOCUS_2006_DFOP <- function() median.A.DFOP <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "A", c(M0, k1, k2, f, DT50, DT90)), "median")) - fit.A.DFOP.r <- as.numeric(c(fit.A.DFOP$bparms.optim, endpoints(fit.A.DFOP)$distimes)) + fit.A.DFOP.r <- as.numeric(c(fit.A.DFOP$bparms.optim, endpoints(fit.A.DFOP)$distimes[c("DT50", "DT90")])) dev.A.DFOP <- abs(round(100 * ((median.A.DFOP - fit.A.DFOP.r)/median.A.DFOP), digits=1)) # about 6.7% deviation for parameter f, the others are < 0.1% checkIdentical(dev.A.DFOP < c(1, 1, 1, 10, 1, 1), rep(TRUE, length(dev.A.DFOP))) @@ -116,7 +116,7 @@ test.FOCUS_2006_DFOP <- function() median.B.DFOP <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "B", c(M0, k1, k2, f, DT50, DT90)), "median")) - fit.B.DFOP.r <- as.numeric(c(fit.B.DFOP$bparms.optim, endpoints(fit.B.DFOP)$distimes)) + fit.B.DFOP.r <- as.numeric(c(fit.B.DFOP$bparms.optim, endpoints(fit.B.DFOP)$distimes[c("DT50", "DT90")])) dev.B.DFOP <- abs(round(100 * ((median.B.DFOP - fit.B.DFOP.r)/median.B.DFOP), digits=1)) # about 0.6% deviation for parameter f, the others are <= 0.1% checkIdentical(dev.B.DFOP < 1, rep(TRUE, length(dev.B.DFOP))) @@ -134,7 +134,7 @@ test.FOCUS_2006_HS <- function() median.A.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "A", c(M0, k1, k2, tb, DT50, DT90)), "median")) - fit.A.HS.r <- as.numeric(c(fit.A.HS$bparms.optim, endpoints(fit.A.HS)$distimes)) + fit.A.HS.r <- as.numeric(c(fit.A.HS$bparms.optim, endpoints(fit.A.HS)$distimes[c("DT50", "DT90")])) dev.A.HS <- abs(round(100 * ((median.A.HS - fit.A.HS.r)/median.A.HS), digits=1)) # about 6.7% deviation for parameter f, the others are < 0.1% checkIdentical(dev.A.HS < 1, rep(TRUE, length(dev.A.HS))) @@ -145,7 +145,7 @@ test.FOCUS_2006_HS <- function() median.B.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "B", c(M0, k1, k2, tb, DT50, DT90)), "median")) - fit.B.HS.r <- as.numeric(c(fit.B.HS$bparms.optim, endpoints(fit.B.HS)$distimes)) + fit.B.HS.r <- as.numeric(c(fit.B.HS$bparms.optim, endpoints(fit.B.HS)$distimes[c("DT50", "DT90")])) dev.B.HS <- abs(round(100 * ((median.B.HS - fit.B.HS.r)/median.B.HS), digits=1)) # < 10% deviation for M0, k1, DT50 and DT90, others are problematic dev.B.HS <- dev.B.HS[c(1, 2, 5, 6)] @@ -157,7 +157,7 @@ test.FOCUS_2006_HS <- function() median.C.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "C", c(M0, k1, k2, tb, DT50, DT90)), "median")) - fit.A.HS.r <- as.numeric(c(fit.A.HS$bparms.optim, endpoints(fit.A.HS)$distimes)) + fit.A.HS.r <- as.numeric(c(fit.A.HS$bparms.optim, endpoints(fit.A.HS)$distimes[c("DT50", "DT90")])) dev.A.HS <- abs(round(100 * ((median.A.HS - fit.A.HS.r)/median.A.HS), digits=1)) # deviation <= 0.1% checkIdentical(dev.A.HS < 1, rep(TRUE, length(dev.A.HS))) @@ -179,7 +179,7 @@ test.FOCUS_2006_SFORB <- function() parent_0 = fit.A.SFORB.1$bparms.optim[[1]], k1 = endpoints(fit.A.SFORB.1)$SFORB[[1]], k2 = endpoints(fit.A.SFORB.1)$SFORB[[2]], - endpoints(fit.A.SFORB.1)$distimes)) + endpoints(fit.A.SFORB.1)$distimes[c("DT50", "DT90")])) dev.A.SFORB.1 <- abs(round(100 * ((median.A.SFORB - fit.A.SFORB.1.r)/median.A.SFORB), digits=1)) # The first Eigenvalue is a lot different from k1 in the DFOP fit # The explanation is that the dataset is simply SFO @@ -190,7 +190,7 @@ test.FOCUS_2006_SFORB <- function() parent_0 = fit.A.SFORB.2$bparms.optim[[1]], k1 = endpoints(fit.A.SFORB.2)$SFORB[[1]], k2 = endpoints(fit.A.SFORB.2)$SFORB[[2]], - endpoints(fit.A.SFORB.2)$distimes)) + endpoints(fit.A.SFORB.2)$distimes[c("DT50", "DT90")])) dev.A.SFORB.2 <- abs(round(100 * ((median.A.SFORB - fit.A.SFORB.2.r)/median.A.SFORB), digits=1)) # The first Eigenvalue is a lot different from k1 in the DFOP fit # The explanation is that the dataset is simply SFO @@ -208,7 +208,7 @@ test.FOCUS_2006_SFORB <- function() parent_0 = fit.B.SFORB.1$bparms.optim[[1]], k1 = endpoints(fit.B.SFORB.1)$SFORB[[1]], k2 = endpoints(fit.B.SFORB.1)$SFORB[[2]], - endpoints(fit.B.SFORB.1)$distimes)) + endpoints(fit.B.SFORB.1)$distimes[c("DT50", "DT90")])) dev.B.SFORB.1 <- abs(round(100 * ((median.B.SFORB - fit.B.SFORB.1.r)/median.B.SFORB), digits=1)) checkIdentical(dev.B.SFORB.1 < 1, rep(TRUE, length(dev.B.SFORB.1))) @@ -216,7 +216,7 @@ test.FOCUS_2006_SFORB <- function() parent_0 = fit.B.SFORB.2$bparms.optim[[1]], k1 = endpoints(fit.B.SFORB.2)$SFORB[[1]], k2 = endpoints(fit.B.SFORB.2)$SFORB[[2]], - endpoints(fit.B.SFORB.2)$distimes)) + endpoints(fit.B.SFORB.2)$distimes[c("DT50", "DT90")])) dev.B.SFORB.2 <- abs(round(100 * ((median.B.SFORB - fit.B.SFORB.2.r)/median.B.SFORB), digits=1)) checkIdentical(dev.B.SFORB.2 < 1, rep(TRUE, length(dev.B.SFORB.2))) } # }}} -- cgit v1.2.1