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-rw-r--r--GNUmakefile4
-rw-r--r--man/plot.mkinfit.Rd3
-rw-r--r--test.log10
-rw-r--r--tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg237
-rw-r--r--tests/figs/plotting/plot-errmod-with-sfo-lin-a-tc.svg235
-rw-r--r--tests/testthat/FOCUS_2006_D.csf2
-rw-r--r--tests/testthat/setup_script.R2
-rw-r--r--tests/testthat/test_error_models.R6
-rw-r--r--tests/testthat/test_plots_summary_twa.R4
9 files changed, 487 insertions, 16 deletions
diff --git a/GNUmakefile b/GNUmakefile
index 0141b54c..231273c1 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -76,6 +76,9 @@ slowtests: install
NOT_CRAN=true "$(RBIN)/Rscript" -e 'library(mkin); testthat::test_dir("tests/testthat/slow")' 2>&1 | tee tests_slow.log
sed -i -e "s/\r.*\r//" tests_slow.log
+vdiffr:
+ "$(RBIN)/Rscript" -e 'vdiffr::manage_cases(filter = "plots|nafta")'
+
testcheck: test check
README.html: README.md
@@ -123,7 +126,6 @@ winbin: $(WINBIN)
dratwin: winbin
"$(RBIN)/Rscript" -e "drat::insertPackage('$(WINBIN)', '~/git/drat/', commit = TRUE)"
-
submit:
@echo "\nHow about make test, make check, make pd, make winbuilder"
@echo "\nIs the DESCRIPTION file up to date?"
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index e7b456a1..fac5663a 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -135,9 +135,6 @@ plot(fit)
plot_res(fit)
plot_err(fit)
-# Show the observed variables separately
-plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright"))
-
# Show the observed variables separately, with residuals
plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"),
show_errmin = TRUE)
diff --git a/test.log b/test.log
index 901091a1..230fbd3b 100644
--- a/test.log
+++ b/test.log
@@ -3,9 +3,9 @@ Testing mkin
✔ | OK F W S | Context
✔ | 2 | Export dataset for reading into CAKE
✔ | 3 | Confidence intervals and p-values
-✔ | 11 | Error model fitting [51.0 s]
+✔ | 10 | Error model fitting [37.0 s]
✔ | 5 | Calculation of FOCUS chi2 error levels [3.5 s]
-✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.5 s]
+✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.4 s]
✔ | 6 | Test fitting the decline of metabolites from their maximum [0.9 s]
✔ | 1 | Fitting the logistic model [0.9 s]
✔ | 1 | Test dataset class mkinds used in gmkin
@@ -15,7 +15,7 @@ Testing mkin
✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.0 s]
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
✔ | 3 | Summary
-✔ | 7 | Plotting [0.4 s]
+✔ | 9 | Plotting [0.5 s]
✔ | 3 | AIC calculation
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s]
✔ | 4 | Fitting the SFORB model [1.7 s]
@@ -23,9 +23,9 @@ Testing mkin
✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.1 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 83.9 s
+Duration: 69.9 s
-OK: 110
+OK: 111
Failed: 0
Warnings: 0
Skipped: 0
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
new file mode 100644
index 00000000..88e7aaee
--- /dev/null
+++ b/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg
@@ -0,0 +1,237 @@
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diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index 171abbb0..638acd88 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: 2019-10-21
+Date: 2019-10-22
Optimiser: IRLS
[Data]
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index d8d94d4b..51fea4f6 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -76,3 +76,5 @@ f_SFO_lin_mkin_OLS <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE)
f_SFO_lin_mkin_ML <- mkinfit(m_synth_SFO_lin, SFO_lin_a, quiet = TRUE,
error_model = "const", error_model_algorithm = "direct")
+fit_obs_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "obs", quiet = TRUE)
+fit_tc_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "tc", quiet = TRUE)
diff --git a/tests/testthat/test_error_models.R b/tests/testthat/test_error_models.R
index d8263c95..12a8b7e5 100644
--- a/tests/testthat/test_error_models.R
+++ b/tests/testthat/test_error_models.R
@@ -20,18 +20,12 @@ context("Error model fitting")
test_that("Error model 'obs' works", {
skip_on_cran()
- fit_obs_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "obs", quiet = TRUE)
parms_2 <- round(fit_obs_1$bparms.optim, c(1, 4, 4, 4, 4, 4))
expect_equivalent(parms_2, c(102.1, 0.7389, 0.2982, 0.0203, 0.7677, 0.7246))
- plot_errmod_fit_obs_1 <- function() plot_err(fit_obs_1, sep_obs = FALSE)
-
- skip_on_travis() # This fails on Travis for an unknown reason
- vdiffr::expect_doppelganger("plot_errmod with SFO_lin_a", plot_errmod_fit_obs_1)
})
test_that("Error model 'tc' works", {
skip_on_cran()
- fit_tc_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "tc", quiet = TRUE)
parms_3 <- round(fit_tc_1$bparms.optim, c(1, 4, 4, 4, 4, 4))
expect_equivalent(parms_3, c(102.1, 0.7393, 0.2992, 0.0202, 0.7687, 0.7229))
})
diff --git a/tests/testthat/test_plots_summary_twa.R b/tests/testthat/test_plots_summary_twa.R
index 089290f6..e3ecbbc4 100644
--- a/tests/testthat/test_plots_summary_twa.R
+++ b/tests/testthat/test_plots_summary_twa.R
@@ -99,6 +99,8 @@ test_that("Plotting mkinfit and mmkin objects is reproducible", {
mmkin_SFO <- function() plot(fits["SFO",])
plot_res_sfo_sfo <- function() plot_res(f_sfo_sfo_desolve)
plot_err_sfo_sfo <- function() plot_err(f_sfo_sfo_desolve)
+ plot_errmod_fit_obs_1 <- function() plot_err(fit_obs_1, sep_obs = FALSE)
+ plot_errmod_fit_tc_1 <- function() plot_err(fit_tc_1, sep_obs = FALSE)
vdiffr::expect_doppelganger("mkinfit plot for FOCUS C with sep = TRUE", plot_sep_FOCUS_C_SFO)
vdiffr::expect_doppelganger("mkinparplot for FOCUS C SFO", mkinparplot_FOCUS_C_SFO)
@@ -107,6 +109,8 @@ test_that("Plotting mkinfit and mmkin objects is reproducible", {
vdiffr::expect_doppelganger("mmkin plot for SFO (FOCUS C and D)", mmkin_SFO)
vdiffr::expect_doppelganger("plot_res for FOCUS D", plot_res_sfo_sfo)
vdiffr::expect_doppelganger("plot_err for FOCUS D", plot_err_sfo_sfo)
+ vdiffr::expect_doppelganger("plot_errmod with SFO_lin_a_obs", plot_errmod_fit_obs_1)
+ vdiffr::expect_doppelganger("plot_errmod with SFO_lin_a_tc", plot_errmod_fit_tc_1)
})
context("AIC calculation")

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