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authorJohannes Ranke <jranke@uni-bremen.de>2019-02-25 17:05:59 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2019-02-25 17:05:59 +0100
commit241f0b977092e4fe106a23ef70506bf37c1a3609 (patch)
treee7a7dfcbfbb5c9d94f1d69c6aca0f08b44627f11
parentaeb6ff55560fa1c704312576be82e3e7ab4ab364 (diff)
Fix tests and add plot and print for nafta
Diffstat
-rw-r--r--build.log3
-rw-r--r--test.log15
-rw-r--r--tests/figs/evaluations-according-to-the-nafta-guidance-from-2015/plot-nafta-analysis-sop-appendix-d.svg450
-rw-r--r--tests/testthat/print_nafta_analysis.txt33
-rw-r--r--tests/testthat/summary_DFOP_FOCUS_C.txt2
-rw-r--r--tests/testthat/test_nafta.R9
-rw-r--r--tests/testthat/test_plots_summary_twa.R4
7 files changed, 505 insertions, 11 deletions
diff --git a/build.log b/build.log
index 6831459d..e7e1addc 100644
--- a/build.log
+++ b/build.log
@@ -7,4 +7,7 @@
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘mkin_0.9.48.1.tar.gz’
+Warnung in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,
+ storing paths of more than 100 bytes is not portable:
+ ‘mkin/tests/figs/evaluations-according-to-the-nafta-guidance-from-2015/plot-nafta-analysis-sop-appendix-d.svg’
diff --git a/test.log b/test.log
index 345746e2..df597cfa 100644
--- a/test.log
+++ b/test.log
@@ -14,17 +14,20 @@ test_logistic.R:41: skip: The logistic fit can be done via differential equation
Skip slow fit of logistic model using deSolve without compilation
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | Model predictions with mkinpredict ⠋ | 1 | Model predictions with mkinpredict ⠙ | 2 | Model predictions with mkinpredict ⠹ | 3 | Model predictions with mkinpredict ✔ | 3 | Model predictions with mkinpredict [0.3 s]
- ⠏ | 0 | Evaluations according to the NAFTA guidance from 2015 ⠋ | 1 | Evaluations according to the NAFTA guidance from 2015 ⠙ | 1 1 | Evaluations according to the NAFTA guidance from 2015 ⠙ | 2 | Evaluations according to the NAFTA guidance from 2015 ⠹ | 3 | Evaluations according to the NAFTA guidance from 2015 ⠸ | 4 | Evaluations according to the NAFTA guidance from 2015 ⠼ | 5 | Evaluations according to the NAFTA guidance from 2015 ⠴ | 6 | Evaluations according to the NAFTA guidance from 2015 ⠦ | 7 | Evaluations according to the NAFTA guidance from 2015 ✔ | 7 | Evaluations according to the NAFTA guidance from 2015 [0.7 s]
- ⠏ | 0 | Fitting of parent only models ⠋ | 1 | Fitting of parent only models ⠙ | 2 | Fitting of parent only models ⠹ | 3 | Fitting of parent only models ⠸ | 4 | Fitting of parent only models ⠼ | 5 | Fitting of parent only models ⠴ | 6 | Fitting of parent only models ⠦ | 7 | Fitting of parent only models ⠧ | 8 | Fitting of parent only models ⠇ | 9 | Fitting of parent only models ⠏ | 10 | Fitting of parent only models ⠋ | 11 | Fitting of parent only models ⠙ | 12 | Fitting of parent only models ⠹ | 13 | Fitting of parent only models ⠸ | 14 | Fitting of parent only models ⠼ | 15 | Fitting of parent only models ⠴ | 16 | Fitting of parent only models ⠦ | 17 | Fitting of parent only models ⠧ | 18 | Fitting of parent only models ⠇ | 19 | Fitting of parent only models ⠏ | 20 | Fitting of parent only models ⠋ | 21 | Fitting of parent only models ✔ | 21 | Fitting of parent only models [23.8 s]
+ ⠏ | 0 | Evaluations according to the NAFTA guidance from 2015 ⠋ | 1 | Evaluations according to the NAFTA guidance from 2015 ⠙ | 1 1 | Evaluations according to the NAFTA guidance from 2015 ⠙ | 2 | Evaluations according to the NAFTA guidance from 2015 ⠹ | 3 | Evaluations according to the NAFTA guidance from 2015 ⠸ | 4 | Evaluations according to the NAFTA guidance from 2015 ⠼ | 5 | Evaluations according to the NAFTA guidance from 2015 ⠴ | 6 | Evaluations according to the NAFTA guidance from 2015 ⠦ | 7 | Evaluations according to the NAFTA guidance from 2015 ⠧ | 8 | Evaluations according to the NAFTA guidance from 2015 ⠇ | 9 | Evaluations according to the NAFTA guidance from 2015 ✔ | 9 | Evaluations according to the NAFTA guidance from 2015 [0.9 s]
+ ⠏ | 0 | Fitting of parent only models ⠋ | 1 | Fitting of parent only models ⠙ | 2 | Fitting of parent only models ⠹ | 3 | Fitting of parent only models ⠸ | 4 | Fitting of parent only models ⠼ | 5 | Fitting of parent only models ⠴ | 6 | Fitting of parent only models ⠦ | 7 | Fitting of parent only models ⠧ | 8 | Fitting of parent only models ⠇ | 9 | Fitting of parent only models ⠏ | 10 | Fitting of parent only models ⠋ | 11 | Fitting of parent only models ⠙ | 12 | Fitting of parent only models ⠹ | 13 | Fitting of parent only models ⠸ | 14 | Fitting of parent only models ⠼ | 15 | Fitting of parent only models ⠴ | 16 | Fitting of parent only models ⠦ | 17 | Fitting of parent only models ⠧ | 18 | Fitting of parent only models ⠇ | 19 | Fitting of parent only models ⠏ | 20 | Fitting of parent only models ⠋ | 21 | Fitting of parent only models ✔ | 21 | Fitting of parent only models [23.9 s]
⠏ | 0 | Calculation of maximum time weighted average concentrations (TWAs) ⠋ | 1 | Calculation of maximum time weighted average concentrations (TWAs) ⠙ | 2 | Calculation of maximum time weighted average concentrations (TWAs) ⠹ | 3 | Calculation of maximum time weighted average concentrations (TWAs) ⠸ | 4 | Calculation of maximum time weighted average concentrations (TWAs) ⠼ | 5 | Calculation of maximum time weighted average concentrations (TWAs) ⠴ | 6 | Calculation of maximum time weighted average concentrations (TWAs) ⠦ | 7 | Calculation of maximum time weighted average concentrations (TWAs) ⠧ | 8 | Calculation of maximum time weighted average concentrations (TWAs) ✔ | 8 | Calculation of maximum time weighted average concentrations (TWAs) [7.2 s]
- ⠏ | 0 | Plotting ⠋ | 1 | Plotting ⠙ | 2 | Plotting ✔ | 2 | Plotting [0.4 s]
+ ⠏ | 0 | Summary ⠋ | 1 | Summary ✔ | 1 | Summary
+ ⠏ | 0 | Plotting ⠋ | 1 | Plotting ⠙ | 2 | Plotting ⠹ | 3 | Plotting ✔ | 3 | Plotting [0.3 s]
+ ⠏ | 0 | Calculation of maximum time weighted average concentrations (TWAs) ⠋ | 1 | Calculation of maximum time weighted average concentrations (TWAs) ⠙ | 2 | Calculation of maximum time weighted average concentrations (TWAs) ⠹ | 3 | Calculation of maximum time weighted average concentrations (TWAs) ⠸ | 4 | Calculation of maximum time weighted average concentrations (TWAs) ⠼ | 5 | Calculation of maximum time weighted average concentrations (TWAs) ⠴ | 6 | Calculation of maximum time weighted average concentrations (TWAs) ⠦ | 7 | Calculation of maximum time weighted average concentrations (TWAs) ⠧ | 8 | Calculation of maximum time weighted average concentrations (TWAs) ✔ | 8 | Calculation of maximum time weighted average concentrations (TWAs) [7.8 s]
+ ⠏ | 0 | Plotting ⠋ | 1 | Plotting ⠙ | 2 | Plotting ⠹ | 3 | Plotting ✔ | 3 | Plotting [0.3 s]
⠏ | 0 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠋ | 1 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠙ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.9 s]
- ⠏ | 0 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.5 s]
+ ⠏ | 0 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.4 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 65.9 s
+Duration: 75.0 s
-OK: 59
+OK: 74
Failed: 0
Warnings: 0
Skipped: 2
diff --git a/tests/figs/evaluations-according-to-the-nafta-guidance-from-2015/plot-nafta-analysis-sop-appendix-d.svg b/tests/figs/evaluations-according-to-the-nafta-guidance-from-2015/plot-nafta-analysis-sop-appendix-d.svg
new file mode 100644
index 00000000..58f57e93
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diff --git a/tests/testthat/print_nafta_analysis.txt b/tests/testthat/print_nafta_analysis.txt
new file mode 100644
index 00000000..61d2539f
--- /dev/null
+++ b/tests/testthat/print_nafta_analysis.txt
@@ -0,0 +1,33 @@
+Sums of squares:
+ SFO IORE DFOP
+1378.6832 615.7730 517.8836
+[1] 717.4598
+
+Parameters:
+$SFO
+ Estimate Pr(>t) Lower Upper
+parent_0 83.755751519 8.076390e-15 76.928220975 90.583282063
+k_parent_sink 0.001703321 7.452357e-05 0.001108568 0.002617164
+
+$IORE
+ Estimate Pr(>t) Lower Upper
+parent_0 9.685291e+01 NA 8.752855e+01 1.061773e+02
+k__iore_parent_sink 8.403374e-14 NA 1.092054e-19 6.466412e-08
+N_parent 6.684458e+00 NA 3.538511e+00 9.830405e+00
+
+$DFOP
+ Estimate Pr(>t) Lower Upper
+parent_0 9.755655e+01 4.439930e-13 8.884447e+01 1.062686e+02
+k1 4.240633e-02 3.554769e-02 1.414189e-02 1.271610e-01
+k2 8.237928e-04 2.060933e-02 3.172784e-04 2.138925e-03
+g 2.881037e-01 1.313715e-04 1.783967e-01 4.299694e-01
+
+
+DTx values:
+ DT50 DT90 DT50_rep
+SFO 407 1352 407
+IORE 541 5192066 1562968
+DFOP 429 2383 841
+
+Representative half-life:
+[1] 841.4096
diff --git a/tests/testthat/summary_DFOP_FOCUS_C.txt b/tests/testthat/summary_DFOP_FOCUS_C.txt
index d8a3e05a..33d55ebc 100644
--- a/tests/testthat/summary_DFOP_FOCUS_C.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_C.txt
@@ -10,7 +10,7 @@ d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
Model predictions using solution type analytical
-Fitted with method Port using 127 model solutions performed in 0.401 s
+Fitted with method Port using test 0 model solutions performed in test time 0 s
Weighting: none
diff --git a/tests/testthat/test_nafta.R b/tests/testthat/test_nafta.R
index 7d650ad8..3615c278 100644
--- a/tests/testthat/test_nafta.R
+++ b/tests/testthat/test_nafta.R
@@ -16,9 +16,6 @@
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>
-library(testthat)
-library(mkin)
-
context("Evaluations according to the NAFTA guidance from 2015")
test_that("Data for more than one compound are rejected",
@@ -31,6 +28,7 @@ test_that("Test data from Appendix D are correctly evaluated", {
dtx_sop <- matrix(c(407, 541, 429, 1352, 5192066, 2383), nrow = 3, ncol = 2)
expect_equivalent(res$distimes[, 1:2], dtx_sop, tolerance = 1,
scale = 1)
+
C0_sop <- c(SFO = 83.8, IORE = 96.9, DFOP = 97.6)
C0_mkin <- sapply(res$parameters, function(x) x["parent_0", "Estimate"])
expect_equivalent(C0_mkin, C0_sop, scale = 1, tolerance = 0.1)
@@ -38,4 +36,9 @@ test_that("Test data from Appendix D are correctly evaluated", {
expect_equal(round(res$S_c), 717)
expect_equal(signif(res$S[["SFO"]], 3), 1.38e+3)
expect_equal(round(res$t_rep), 841)
+
+ expect_known_output(print(res), "print_nafta_analysis.txt")
+
+ plot_nafta <- function() plot(res)
+ vdiffr::expect_doppelganger("Plot NAFTA analysis SOP Appendix D", plot_nafta)
})
diff --git a/tests/testthat/test_plots_summary_twa.R b/tests/testthat/test_plots_summary_twa.R
index 83a6a040..d5f4f199 100644
--- a/tests/testthat/test_plots_summary_twa.R
+++ b/tests/testthat/test_plots_summary_twa.R
@@ -53,11 +53,13 @@ context("Summary")
test_that("The summary is reproducible", {
skip_on_cran()
fit <- fits[["DFOP", "FOCUS_C"]]
- undebug(summary.mkinfit)
+ test_summary <- summary(fit)
test_summary$fit_version <- "Dummy 0.0 for testing"
test_summary$fit_Rversion <- "Dummy R version for testing"
test_summary$date.fit <- "Dummy date for testing"
test_summary$date.summary <- "Dummy date for testing"
+ test_summary$calls <- "test 0"
+ test_summary$time <- c(elapsed = "test time 0")
expect_known_output(print(test_summary), "summary_DFOP_FOCUS_C.txt")
})

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