Skip more tests on CRANv0.9.47.5

Static documentation rebuilt by pkgdown

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]]