Skip some tests on CRAN, more quiet examplesv0.9.47.1

3 files changed, 37 insertions, 40 deletions

diff --git a/tests/testthat/test_irls.R b/tests/testthat/test_irls.R
index 0b005182..6389b662 100644
--- a/tests/testthat/test_irls.R
+++ b/tests/testthat/test_irls.R
@@ -34,12 +34,14 @@ SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
 DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
 
 test_that("Reweighting method 'obs' works", {
+  skip_on_cran()
   fit_irls_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, reweight.method = "obs", quiet = TRUE)
   parms_1 <- round(fit_irls_1$bparms.optim, c(1, 4, 4, 4, 4, 4))
   expect_equivalent(parms_1, c(102.1, 0.7389, 0.2982, 0.0203, 0.7677, 0.7246))
 })
 
 test_that("Reweighting method 'tc' works", {
+  skip_on_cran()
   fit_irls_2 <- mkinfit(m_synth_DFOP_par, DFOP_par_c, reweight.method = "tc", quiet = TRUE)
   parms_2 <- signif(fit_irls_2$bparms.optim, 3)
   expect_equivalent(parms_2, c(99.3, 0.041, 0.00962, 0.597, 0.393, 0.298, 0.0203, 0.707))
diff --git a/tests/testthat/test_schaefer07_complex_case.R b/tests/testthat/test_schaefer07_complex_case.R
index 1b51e5d2..80306bbe 100644
--- a/tests/testthat/test_schaefer07_complex_case.R
+++ b/tests/testthat/test_schaefer07_complex_case.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2014-2015 Johannes Ranke

+# Copyright (C) 2014-2015,2018 Johannes Ranke

 # Contact: jranke@uni-bremen.de

 

 # This file is part of the R package mkin

@@ -20,19 +20,20 @@
 

 context("Complex test case from Schaefer et al. (2007) Piacenza paper")

 

-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", quiet = TRUE)

+test_that("Complex test case from Schaefer (2007) can be reproduced (10% tolerance)", {

+  

+  skip_on_cran()         

+  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", quiet = TRUE)

 

-schaefer07_long <- mkin_wide_to_long(schaefer07_complex_case, time = "time")

+  schaefer07_long <- mkin_wide_to_long(schaefer07_complex_case, time = "time")

 

-fit.default <- mkinfit(schaefer07_complex_model, schaefer07_long, quiet = TRUE)

+  fit.default <- mkinfit(schaefer07_complex_model, schaefer07_long, quiet = TRUE)

 

-test_that("Complex test case from Schaefer (2007) can be reproduced (10% tolerance)", {

-  

   s <- summary(fit.default)

   r <- schaefer07_complex_results

 

@@ -57,12 +58,11 @@ test_that("Complex test case from Schaefer (2007) can be reproduced (10% toleran
   r$means <- (r$KinGUI + r$ModelMaker)/2

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

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

-})

 

-test_that("We avoid the local minumum with default settings", {

   # If we use optimisation algorithm 'Marq' we get a local minimum with a

   # sum of squared residuals of 273.3707

   # When using 'Marq', we need to give a good starting estimate e.g. for k_A2 in

   # order to get the optimum with sum of squared residuals 240.5686

   expect_equal(round(fit.default$ssr, 4), 240.5686)

 })

+

diff --git a/tests/testthat/test_synthetic_data_for_UBA_2014.R b/tests/testthat/test_synthetic_data_for_UBA_2014.R
index ea762353..fd3e8bba 100644
--- a/tests/testthat/test_synthetic_data_for_UBA_2014.R
+++ b/tests/testthat/test_synthetic_data_for_UBA_2014.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
@@ -19,46 +19,41 @@
 context("Results for synthetic data established in expertise for UBA (Ranke 2014)")
 
 
-m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
-                           M1 = mkinsub("SFO", "M2"),
-                           M2 = mkinsub("SFO"),
-                           use_of_ff = "max", quiet = TRUE)
+test_that("Results are correct for SFO_lin_a", {
+  m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
+                             M1 = mkinsub("SFO", "M2"),
+                             M2 = mkinsub("SFO"),
+                             use_of_ff = "max", quiet = TRUE)
+  fit_SFO_lin_a <- mkinfit(m_synth_SFO_lin, 
+                           synthetic_data_for_UBA_2014[[1]]$data, 
+                           quiet = TRUE)
+  # Results for SFO_lin_a from p. 48
 
-m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
-                           M1 = mkinsub("SFO"),
-                           M2 = mkinsub("SFO"),
-                           use_of_ff = "max", quiet = TRUE)
-
-fit_SFO_lin_a <- mkinfit(m_synth_SFO_lin, 
-                         synthetic_data_for_UBA_2014[[1]]$data, 
-                         quiet = TRUE)
-fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, 
-                          synthetic_data_for_UBA_2014[[12]]$data,
-                          quiet = TRUE)
-
-# Results for SFO_lin_a from p. 48
-
-test_that("Fitted parameters are correct for SFO_lin_a", {
   parms <- round(fit_SFO_lin_a$bparms.optim, c(1, 4, 4, 4, 4, 4))
   expect_equivalent(parms, c(102.1, 0.7393, 0.2992, 0.0202, 0.7687, 0.7229))
-})
-
-test_that("FOCUS chi2 error levels are correct for SFO_lin_a", {
   errmin <- round(100 * mkinerrmin(fit_SFO_lin_a)$err.min, 2)
   expect_equivalent(errmin, c(8.45, 8.66, 10.58, 3.59))
 })
 
 # Results for DFOP_par_c from p. 54
 
-test_that("Fitted parameters are correct for DFOP_par_c", {
+test_that("Results are correct for DFOP_par_c", {
+  skip_on_cran()          
+  m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
+                             M1 = mkinsub("SFO"),
+                             M2 = mkinsub("SFO"),
+                             use_of_ff = "max", quiet = TRUE)
+
+
+  fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, 
+                            synthetic_data_for_UBA_2014[[12]]$data,
+                            quiet = TRUE)
+
   parms <- round(fit_DFOP_par_c$bparms.optim, c(1, 4, 4, 4, 4, 4, 4, 4))
   expect_equal(parms, c(parent_0 = 103.0, 
                         k_M1 = 0.0389, k_M2 = 0.0095,
                         f_parent_to_M1 = 0.5565, f_parent_to_M2 = 0.3784,
                         k1 = 0.3263, k2 = 0.0202, g = 0.7130))
-})
-
-test_that("FOCUS chi2 error levels are correct for DFOP_par_c", {
   errmin <- round(100 * mkinerrmin(fit_DFOP_par_c)$err.min, 2)
   expect_equivalent(errmin, c(4.03, 3.05, 5.07, 3.17))
 })