Start of migration from RUnit to testthat

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diff --git a/tests/testthat/runit.mkinfit.R b/tests/testthat/runit.mkinfit.R
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+# Copyright (C) 2010-2014 Johannes Ranke

+# Contact: jranke@uni-bremen.de

+

+# This file is part of the R package mkin

+

+# mkin is free software: you can redistribute it and/or modify it under the

+# terms of the GNU General Public License as published by the Free Software

+# Foundation, either version 3 of the License, or (at your option) any later

+# version.

+

+# This program is distributed in the hope that it will be useful, but WITHOUT

+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS

+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more

+# details.

+

+# You should have received a copy of the GNU General Public License along with

+# this program. If not, see <http://www.gnu.org/licenses/>

+

+# Test SFO model to a relative tolerance of 1% # {{{

+test.FOCUS_2006_SFO <- function()

+{

+  SFO.1 <- mkinmod(parent = list(type = "SFO"))

+  SFO.2 <- mkinmod(parent = list(type = "SFO"), use_of_ff = "max")

+

+  fit.A.SFO.1 <- mkinfit(SFO.1, FOCUS_2006_A, quiet=TRUE)

+  fit.A.SFO.2 <- mkinfit(SFO.2, FOCUS_2006_A, quiet=TRUE)

+

+  median.A.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F, dataset == "A", 

+                   c(M0, k, DT50, DT90)), "median"))

+

+  fit.A.SFO.1.r <- as.numeric(c(fit.A.SFO.1$bparms.optim, endpoints(fit.A.SFO.1)$distimes))

+  dev.A.SFO.1 <- abs(round(100 * ((median.A.SFO - fit.A.SFO.1.r)/median.A.SFO), digits=1))

+  checkIdentical(dev.A.SFO.1 < 1, rep(TRUE, length(dev.A.SFO.1)))

+

+  fit.A.SFO.2.r <- as.numeric(c(fit.A.SFO.2$bparms.optim, endpoints(fit.A.SFO.2)$distimes))

+  dev.A.SFO.2 <- abs(round(100 * ((median.A.SFO - fit.A.SFO.2.r)/median.A.SFO), digits=1))

+  checkIdentical(dev.A.SFO.2 < 1, rep(TRUE, length(dev.A.SFO.2)))

+

+  fit.C.SFO.1 <- mkinfit(SFO.1, FOCUS_2006_C, quiet=TRUE)

+  fit.C.SFO.2 <- mkinfit(SFO.2, FOCUS_2006_C, quiet=TRUE)

+

+  median.C.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F, dataset == "C", 

+                   c(M0, k, DT50, DT90)), "median"))

+

+  fit.C.SFO.1.r <- as.numeric(c(fit.C.SFO.1$bparms.optim, endpoints(fit.C.SFO.1)$distimes))

+  dev.C.SFO.1 <- abs(round(100 * ((median.C.SFO - fit.C.SFO.1.r)/median.C.SFO), digits=1))

+  checkIdentical(dev.C.SFO.1 < 1, rep(TRUE, length(dev.C.SFO.1)))

+

+  fit.C.SFO.2.r <- as.numeric(c(fit.C.SFO.2$bparms.optim, endpoints(fit.C.SFO.2)$distimes))

+  dev.C.SFO.2 <- abs(round(100 * ((median.C.SFO - fit.C.SFO.2.r)/median.C.SFO), digits=1))

+  checkIdentical(dev.C.SFO.2 < 1, rep(TRUE, length(dev.C.SFO.2)))

+} # }}}

+

+# Test FOMC model to a relative tolerance of 1% {{{

+# See kinfit vignette for a discussion of FOMC fits to FOCUS_2006_A

+# In this case, only M0, DT50 and DT90 are checked

+test.FOCUS_2006_FOMC <- function()

+{

+  FOMC <- mkinmod(parent = list(type = "FOMC"))

+

+  # FOCUS_2006_A (compare kinfit vignette for discussion) 

+  fit.A.FOMC <- mkinfit(FOMC, FOCUS_2006_A, quiet=TRUE)

+

+  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[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)))

+

+  # FOCUS_2006_B

+  fit.B.FOMC <- mkinfit(FOMC, FOCUS_2006_B, quiet=TRUE)

+

+  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[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)))

+

+  # FOCUS_2006_C

+  fit.C.FOMC <- mkinfit(FOMC, FOCUS_2006_C, quiet=TRUE)

+

+  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[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)))

+} # }}}

+

+# Test DFOP model, tolerance of 1% with the exception of f parameter for A {{{

+test.FOCUS_2006_DFOP <- function()

+{

+  DFOP <- mkinmod(parent = list(type = "DFOP"))

+

+  # FOCUS_2006_A

+  # Results were too much dependent on algorithm, as this dataset

+  # is pretty much SFO. "Port" gave a lower deviance, but deviated from the

+  # median of FOCUS_2006 solutions

+

+  # FOCUS_2006_B

+  fit.B.DFOP <- mkinfit(DFOP, FOCUS_2006_B, quiet=TRUE)

+

+  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[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)))

+} # }}}

+

+# Test HS model to a relative tolerance of 1% excluding Mathematica values {{{

+# as they are unreliable

+test.FOCUS_2006_HS <- function()

+{

+  HS <- mkinmod(parent = list(type = "HS"))

+

+  # FOCUS_2006_A

+  fit.A.HS <- mkinfit(HS, FOCUS_2006_A, quiet=TRUE)

+

+  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[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)))

+

+  # FOCUS_2006_B

+  fit.B.HS <- mkinfit(HS, FOCUS_2006_B, quiet=TRUE)

+

+  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[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)]

+  checkIdentical(dev.B.HS < 10, rep(TRUE, length(dev.B.HS)))

+

+  # FOCUS_2006_C

+  fit.C.HS <- mkinfit(HS, FOCUS_2006_C, quiet=TRUE)

+

+  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.C.HS.r <- as.numeric(c(fit.C.HS$bparms.optim, endpoints(fit.C.HS)$distimes[c("DT50", "DT90")]))

+  dev.C.HS <- abs(round(100 * ((median.C.HS - fit.C.HS.r)/median.C.HS), digits=1))

+  # deviation <= 0.1%

+  checkIdentical(dev.C.HS < 1, rep(TRUE, length(dev.C.HS)))

+} # }}}

+

+# Test SFORB model against DFOP solutions to a relative tolerance of 1% # {{{

+test.FOCUS_2006_SFORB <- function()

+{

+  SFORB <- mkinmod(parent = list(type = "SFORB"))

+

+  # FOCUS_2006_A

+  # Again it does not make a lot of sense to use a SFO dataset for this

+

+  # FOCUS_2006_B

+  fit.B.SFORB.1 <- mkinfit(SFORB, FOCUS_2006_B, quiet=TRUE)

+  fit.B.SFORB.2 <- mkinfit(SFORB, FOCUS_2006_B, solution_type = "deSolve", quiet=TRUE)

+

+  median.B.SFORB <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "B", 

+                   c(M0, k1, k2, DT50, DT90)), "median"))

+

+  fit.B.SFORB.1.r <- as.numeric(c(

+                      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[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)))

+

+  fit.B.SFORB.2.r <- as.numeric(c(

+                      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[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)))

+} # }}}

+

+# Test eigenvalue based fit to Schaefer 2007 data against solution from conference paper {{{

+test.mkinfit.schaefer07_complex_example <- function()

+{

+  schaefer07_complex_model <- mkinmod(

+    parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),

+    A1 = list(type = "SFO", to = "A2"),

+    B1 = list(type = "SFO"),

+    C1 = list(type = "SFO"),

+    A2 = list(type = "SFO"), use_of_ff = "max")

+  

+  # If we use the default algorithm 'Marq' we need to give a good starting 

+  # estimate for k_A2 in order to find the solution published by Schaefer et al.

+  fit <- mkinfit(schaefer07_complex_model, method.modFit = "Port",

+    mkin_wide_to_long(schaefer07_complex_case, time = "time"))

+  s <- summary(fit)

+  r <- schaefer07_complex_results

+  attach(as.list(fit$bparms.optim))

+  r$mkin <- c(

+    k_parent,

+    s$distimes["parent", "DT50"],

+    s$ff["parent_A1"],

+    k_A1,

+    s$distimes["A1", "DT50"],

+    s$ff["parent_B1"],

+    k_B1,

+    s$distimes["B1", "DT50"],

+    s$ff["parent_C1"],

+    k_C1,

+    s$distimes["C1", "DT50"],

+    s$ff["A1_A2"],

+    k_A2,

+    s$distimes["A2", "DT50"])

+  r$means <- (r$KinGUI + r$ModelMaker)/2

+  r$mkin.deviation <- abs(round(100 * ((r$mkin - r$means)/r$means), digits=1))

+  checkIdentical(r$mkin.deviation < 10, rep(TRUE, 14))

+} # }}}

+

+# vim: set foldmethod=marker ts=2 sw=2 expandtab: