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-rw-r--r--man/summary.saem.mmkin.Rd3
-rw-r--r--test_dev.log18
-rw-r--r--tests/figs/deps.txt2
-rw-r--r--tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg2
-rw-r--r--tests/testthat/FOCUS_2006_D.csf2
-rw-r--r--tests/testthat/test_nafta.R2
-rw-r--r--tests/testthat/test_plot.R1
7 files changed, 17 insertions, 13 deletions
diff --git a/man/summary.saem.mmkin.Rd b/man/summary.saem.mmkin.Rd
index f3e3fde3..67cb3cbb 100644
--- a/man/summary.saem.mmkin.Rd
+++ b/man/summary.saem.mmkin.Rd
@@ -87,7 +87,8 @@ ds_syn_dfop_sfo <- lapply(ds_mean_dfop_sfo, function(ds) {
\dontrun{
# Evaluate using mmkin and saem
-f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo, quiet = TRUE, error_model = "tc", cores = 5)
+f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo,
+ quiet = TRUE, error_model = "tc", cores = 5)
f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo)
summary(f_saem_dfop_sfo, data = TRUE)
}
diff --git a/test_dev.log b/test_dev.log
index b5f8fd8e..c57bb958 100644
--- a/test_dev.log
+++ b/test_dev.log
@@ -3,14 +3,14 @@ Testing mkin
✔ | OK F W S | Context
✔ | 4 | AIC calculation
✔ | 2 | Export dataset for reading into CAKE
-✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8 s]
+✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9 s]
✔ | 4 | Calculation of FOCUS chi2 error levels [0.4 s]
-✔ | 7 | Fitting the SFORB model [3.0 s]
-✔ | 5 | Analytical solutions for coupled models [2.9 s]
+✔ | 7 | Fitting the SFORB model [3.1 s]
+✔ | 5 | Analytical solutions for coupled models [2.8 s]
✔ | 5 | Calculation of Akaike weights
✔ | 10 | Confidence intervals and p-values [0.9 s]
-✔ | 14 | Error model fitting [3.4 s]
-✔ | 4 | Test fitting the decline of metabolites from their maximum [0.2 s]
+✔ | 14 | Error model fitting [3.8 s]
+✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s]
✔ | 1 | Fitting the logistic model [0.2 s]
✔ | 1 | Test dataset class mkinds used in gmkin
✔ | 1 | mkinfit features [0.2 s]
@@ -18,18 +18,18 @@ Testing mkin
✔ | 8 | mkinmod model generation and printing [0.2 s]
✔ | 3 | Model predictions with mkinpredict [0.3 s]
✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.3 s]
-✔ | 9 | Nonlinear mixed-effects models [7.0 s]
+✔ | 9 | Nonlinear mixed-effects models [7.3 s]
✔ | 14 | Plotting [1.3 s]
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.3 s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4 s]
✔ | 4 | Summary
✔ | 1 | Summaries of old mkinfit objects
✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.0 s]
-✔ | 9 | Hypothesis tests [7.1 s]
+✔ | 9 | Hypothesis tests [7.4 s]
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 35.6 s
+Duration: 36.9 s
OK: 162
Failed: 0
diff --git a/tests/figs/deps.txt b/tests/figs/deps.txt
index fa7c5968..8d7f66b6 100644
--- a/tests/figs/deps.txt
+++ b/tests/figs/deps.txt
@@ -1,3 +1,3 @@
- vdiffr-svg-engine: 1.0
-- vdiffr: 0.3.2
+- vdiffr: 0.3.3
- freetypeharfbuzz: 0.2.5
diff --git a/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg b/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg
index 8c234234..d8e3644b 100644
--- a/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg
+++ b/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg
@@ -222,7 +222,7 @@
<line x1='451.66' y1='486.94' x2='451.66' y2='479.30' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' />
<line x1='447.84' y1='480.11' x2='455.47' y2='480.11' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' />
<line x1='451.66' y1='483.93' x2='451.66' y2='476.29' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' />
-<line x1='437.55' y1='249.04' x2='445.19' y2='249.04' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' />
+<line x1='437.55' y1='249.05' x2='445.19' y2='249.05' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' />
<line x1='441.37' y1='252.86' x2='441.37' y2='245.23' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' />
<line x1='437.55' y1='423.26' x2='445.19' y2='423.26' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' />
<line x1='441.37' y1='427.07' x2='441.37' y2='419.44' style='stroke-width: 0.75; stroke: #61D04F;' clip-path='url(#cpNDE5LjA0fDY4OS43Nnw1MDIuNTZ8NTkuMDQ=)' />
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index a0e63657..7d562426 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -5,7 +5,7 @@ Description:
MeasurementUnits: % AR
TimeUnits: days
Comments: Created using mkin::CAKE_export
-Date: 2020-11-08
+Date: 2020-11-11
Optimiser: IRLS
[Data]
diff --git a/tests/testthat/test_nafta.R b/tests/testthat/test_nafta.R
index 62c88983..fcab4ffb 100644
--- a/tests/testthat/test_nafta.R
+++ b/tests/testthat/test_nafta.R
@@ -20,6 +20,7 @@ test_that("Test data from Appendix B are correctly evaluated", {
expect_known_output(print(res), "NAFTA_SOP_Appendix_B.txt")
+ skip_on_travis()
plot_nafta <- function() plot(res)
if(requireNamespace("vdiffr", quietly = TRUE)) {
skip_if(getRversion() < "4.1.0")
@@ -48,6 +49,7 @@ test_that("Test data from Appendix D are correctly evaluated", {
expect_known_output(print(res), "NAFTA_SOP_Appendix_D.txt")
+ skip_on_travis()
plot_nafta <- function() plot(res)
if(requireNamespace("vdiffr", quietly = TRUE)) {
skip_if(getRversion() < "4.1.0")
diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R
index 40d5928f..587ec02e 100644
--- a/tests/testthat/test_plot.R
+++ b/tests/testthat/test_plot.R
@@ -2,6 +2,7 @@ context("Plotting")
test_that("Plotting mkinfit and mmkin objects is reproducible", {
skip_on_cran()
+ skip_on_travis()
plot_default_FOCUS_C_SFO <- function() plot(fits[["SFO", "FOCUS_C"]])
plot_res_FOCUS_C_SFO <- function() plot(fits[["SFO", "FOCUS_C"]], show_residuals = TRUE)
plot_res_FOCUS_C_SFO_2 <- function() plot_res(fits[["SFO", "FOCUS_C"]])

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