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-rw-r--r--tests/testthat/test_FOCUS_D_UBA_expertise.R70
-rw-r--r--tests/testthat/test_mkinpredict_SFO_SFO.R4
-rw-r--r--tests/testthat/test_parent_only.R3
-rw-r--r--tests/testthat/test_synthetic_data_for_UBA_2014.R1
-rw-r--r--tests/testthat/test_twa.R8
5 files changed, 40 insertions, 46 deletions
diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R
index 5d5a801a..3b241aa4 100644
--- a/tests/testthat/test_FOCUS_D_UBA_expertise.R
+++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2015 Johannes Ranke
+# Copyright (C) 2015,2018 Johannes Ranke
# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
@@ -18,69 +18,59 @@
context("Results for FOCUS D established in expertise for UBA (Ranke 2014)")
-SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
- m1 = list(type = "SFO"), quiet = TRUE)
-SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
- m1 = list(type = "SFO"),
- use_of_ff = "max", quiet = TRUE)
+# Results are from p. 40
-fit.default <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
-fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
+test_that("Fits without formation fractions are correct for FOCUS D", {
+ SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
+ m1 = list(type = "SFO"), quiet = TRUE)
+ fit.default <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
-# Results are from p. 40
+ expect_equal(round(as.numeric(endpoints(fit.default)$distimes["parent", ]), 2),
+ c(7.02, 23.33))
+ expect_equal(round(as.numeric(endpoints(fit.default)$distimes["m1", ]), 1),
+ c(131.8, 437.7))
-test_that("Fitted parameters are correct for FOCUS D", {
+ expect_equal(signif(summary(fit.default)$bpar[, "t value"], 5),
+ c(parent_0 = 61.720, k_parent_sink = 12.777, k_parent_m1 = 24.248, k_m1_sink = 7.3486))
+})
+
+test_that("Fits with formation fractions are correct for FOCUS D", {
+ skip_on_cran()
+ SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
+ m1 = list(type = "SFO"),
+ use_of_ff = "max", quiet = TRUE)
+
+ fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
expect_equivalent(round(fit.ff$bparms.optim, c(2, 4, 4, 4)),
c(99.60, 0.0987, 0.0053, 0.5145))
-})
-test_that("FOCUS chi2 error levels are correct for FOCUS D", {
expect_equivalent(round(100 * mkinerrmin(fit.ff)$err.min, 2),
c(6.40, 6.46, 4.69))
-})
-test_that("DT50/90 are correct for FOCUS D when using formation fractions", {
expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["parent", ]), 2),
c(7.02, 23.33))
expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["m1", ]), 1),
c(131.8, 437.7))
})
-test_that("DT50/90 are correct for FOCUS D when not using formation fractions", {
- expect_equal(round(as.numeric(endpoints(fit.default)$distimes["parent", ]), 2),
- c(7.02, 23.33))
- expect_equal(round(as.numeric(endpoints(fit.default)$distimes["m1", ]), 1),
- c(131.8, 437.7))
-})
-
# References:
# Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative
# zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452
-context("The t-test for significant difference from zero")
-
-test_that("The t-value for fits using internal transformations corresponds with result from FME", {
-
- expect_equal(signif(summary(fit.default)$bpar[, "t value"], 5),
- c(parent_0 = 61.720, k_parent_sink = 12.777, k_parent_m1 = 24.248, k_m1_sink = 7.3486))
-
-})
-
-m_synth_DFOP_par.minff <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
- M1 = mkinsub("SFO"),
- M2 = mkinsub("SFO"),
- use_of_ff = "min", quiet = TRUE)
-
-fit_DFOP_par_c_2 <- mkinfit(m_synth_DFOP_par.minff,
- synthetic_data_for_UBA_2014[[12]]$data,
- quiet = TRUE)
-
test_that("The t-value for fits using internal transformations corresponds with results from FME, synthetic data", {
+ skip_on_cran()
+ m_synth_DFOP_par.minff <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
+ M1 = mkinsub("SFO"),
+ M2 = mkinsub("SFO"),
+ use_of_ff = "min", quiet = TRUE)
+
+ fit_DFOP_par_c_2 <- mkinfit(m_synth_DFOP_par.minff,
+ synthetic_data_for_UBA_2014[[12]]$data,
+ quiet = TRUE)
# Note that the k1 and k2 are exchanged in the untransformed fit evaluated with FME for this test
expect_equal(signif(summary(fit_DFOP_par_c_2)$bpar[1:7, "t value"], 5),
c(parent_0 = 80.054, k_M1_sink = 12.291, k_M2_sink = 10.588,
f_parent_to_M1 = 21.4960, f_parent_to_M2 = 24.0890,
k1 = 16.1450, k2 = 8.1747))
-
})
diff --git a/tests/testthat/test_mkinpredict_SFO_SFO.R b/tests/testthat/test_mkinpredict_SFO_SFO.R
index b7004f64..3fcdb3a2 100644
--- a/tests/testthat/test_mkinpredict_SFO_SFO.R
+++ b/tests/testthat/test_mkinpredict_SFO_SFO.R
@@ -1,6 +1,4 @@
-# $Id: jranke $
-
-# Copyright (C) 2012-2015 Johannes Ranke
+# Copyright (C) 2012-2015,2018 Johannes Ranke
# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
diff --git a/tests/testthat/test_parent_only.R b/tests/testthat/test_parent_only.R
index ee0cc144..7521e145 100644
--- a/tests/testthat/test_parent_only.R
+++ b/tests/testthat/test_parent_only.R
@@ -165,6 +165,7 @@ test_that("Fits for FOCUS C deviate less than 0.1% from median of values from FO
})
test_that("SFO fits give approximately (0.001%) equal results with different solution methods", {
+ skip_on_cran()
fit.A.SFO.default <- mkinfit("SFO", FOCUS_2006_A, quiet = TRUE)$bparms.optim
fits.A.SFO <- list()
@@ -179,6 +180,7 @@ test_that("SFO fits give approximately (0.001%) equal results with different sol
})
test_that("FOMC fits give approximately (0.001%) equal results with different solution methods", {
+ skip_on_cran()
fit.C.FOMC.default <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)$bparms.optim
fits.C.FOMC <- list()
@@ -191,6 +193,7 @@ test_that("FOMC fits give approximately (0.001%) equal results with different so
})
test_that("DFOP fits give approximately (0.001%) equal results with different solution methods", {
+ skip_on_cran()
fit.C.DFOP.default <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE)$bparms.optim
fits.C.DFOP <- list()
diff --git a/tests/testthat/test_synthetic_data_for_UBA_2014.R b/tests/testthat/test_synthetic_data_for_UBA_2014.R
index fd3e8bba..6856a9a3 100644
--- a/tests/testthat/test_synthetic_data_for_UBA_2014.R
+++ b/tests/testthat/test_synthetic_data_for_UBA_2014.R
@@ -20,6 +20,7 @@ context("Results for synthetic data established in expertise for UBA (Ranke 2014
test_that("Results are correct for SFO_lin_a", {
+ skip_on_cran()
m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
M1 = mkinsub("SFO", "M2"),
M2 = mkinsub("SFO"),
diff --git a/tests/testthat/test_twa.R b/tests/testthat/test_twa.R
index d5c0b98b..a84b2c4e 100644
--- a/tests/testthat/test_twa.R
+++ b/tests/testthat/test_twa.R
@@ -18,11 +18,13 @@
context("Calculation of maximum time weighted average concentrations (TWAs)")
-twa_models <- c("SFO", "FOMC", "DFOP")
-fits <- mmkin(twa_models, list(FOCUS_D = FOCUS_2006_D),
- quiet = TRUE, cores = 1)
test_that("Time weighted average concentrations are correct", {
+ skip_on_cran()
+ twa_models <- c("SFO", "FOMC", "DFOP")
+ fits <- mmkin(twa_models, list(FOCUS_D = FOCUS_2006_D),
+ quiet = TRUE, cores = 1)
+
outtimes_7 <- seq(0, 7, length.out = 10000)
for (model in twa_models) {
fit <- fits[[model, 1]]

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