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-rw-r--r--R/nafta.R3
-rw-r--r--build.log1
-rw-r--r--data/NAFTA_2015.rdabin264 -> 0 bytes
-rw-r--r--data/NAFTA_SOP_2015.rdabin0 -> 390 bytes
-rw-r--r--man/NAFTA_SOP_2015.Rd (renamed from man/NAFTA_2015_datasets.Rd)15
-rw-r--r--man/nafta.Rd2
-rw-r--r--test.log43
-rw-r--r--tests/figs/evaluations-according-to-2015-nafta-guidance/nafta-sop-appendix-b.svg462
-rw-r--r--tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg85
-rw-r--r--tests/testthat/FOCUS_2006_D.csf2
-rw-r--r--tests/testthat/NAFTA_SOP_Appendix_B.txt35
-rw-r--r--tests/testthat/NAFTA_SOP_Appendix_D.txt (renamed from tests/testthat/print_nafta_analysis.txt)2
-rw-r--r--tests/testthat/test_CAKE_export.R22
-rw-r--r--tests/testthat/test_nafta.R28
14 files changed, 647 insertions, 53 deletions
diff --git a/R/nafta.R b/R/nafta.R
index 2af2404f..03bd77c1 100644
--- a/R/nafta.R
+++ b/R/nafta.R
@@ -49,7 +49,7 @@ nafta <- function(ds, title = NA, quiet = FALSE) {
result$S["IORE"]
result$S_c <- result$S[["IORE"]] * (1 + p/(n - p) * qf(0.5, p, n - p))
- result$t_rep <- .evaluate_nafta_results(result$S, result$S_c,
+ result$t_rep <- .evaluate_nafta_results(result$S, result$S_c,
result$distimes, quiet = quiet)
class(result) <- "nafta"
@@ -67,6 +67,7 @@ plot.nafta <- function(x, legend = FALSE, main = "auto", ...) {
print.nafta <- function(x, quiet = TRUE, ...) {
cat("Sums of squares:\n")
print(x$S)
+ cat("\nCritical sum of squares for checking the SFO model:\n")
print(x$S_c)
cat("\nParameters:\n")
print(x$parameters)
diff --git a/build.log b/build.log
index 6831459d..217b621f 100644
--- a/build.log
+++ b/build.log
@@ -5,6 +5,7 @@
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
+Removed empty directory ‘mkin/tests/figs/export-dataset-for-reading-into-cake’
* looking to see if a ‘data/datalist’ file should be added
* building ‘mkin_0.9.48.1.tar.gz’
diff --git a/data/NAFTA_2015.rda b/data/NAFTA_2015.rda
deleted file mode 100644
index 48183048..00000000
--- a/data/NAFTA_2015.rda
+++ /dev/null
Binary files differ
diff --git a/data/NAFTA_SOP_2015.rda b/data/NAFTA_SOP_2015.rda
new file mode 100644
index 00000000..eb7ce63f
--- /dev/null
+++ b/data/NAFTA_SOP_2015.rda
Binary files differ
diff --git a/man/NAFTA_2015_datasets.Rd b/man/NAFTA_SOP_2015.Rd
index 4ca494ee..a47ae155 100644
--- a/man/NAFTA_2015_datasets.Rd
+++ b/man/NAFTA_SOP_2015.Rd
@@ -1,15 +1,16 @@
-\name{NAFTA_2015_datasets}
-\alias{MRID_555555}
+\name{NAFTA_SOP_2015}
+\alias{NAFTA_SOP_Appendix_B}
+\alias{NAFTA_SOP_Appendix_D}
\docType{data}
\title{
-Example datasets from the NAFTA guidance published 2015
+Example datasets from the NAFTA SOP published 2015
}
\description{
-Data taken from US EPA (2015), p. 23.
+Data taken from US EPA (2015), p. 19 and 23.
}
-\usage{NAFTA_2015_datasets}
+\usage{NAFTA_SOP_2015}
\format{
- 1 dataset with observations on the following variables.
+ 2 datasets with observations on the following variables.
\describe{
\item{\code{name}}{a factor containing the name of the observed variable}
\item{\code{time}}{a numeric vector containing time points}
@@ -28,7 +29,7 @@ Data taken from US EPA (2015), p. 23.
\url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance}
}
\examples{
- nafta_evaluation <- nafta(MRID_555555)
+ nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D)
print(nafta_evaluation)
plot(nafta_evaluation)
}
diff --git a/man/nafta.Rd b/man/nafta.Rd
index cd06e02b..48b4fefe 100644
--- a/man/nafta.Rd
+++ b/man/nafta.Rd
@@ -39,7 +39,7 @@ nafta(ds, title = NA, quiet = FALSE)
\url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance}
}
\examples{
- nafta_evaluation <- nafta(MRID_555555)
+ nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D)
print(nafta_evaluation)
plot(nafta_evaluation)
}
diff --git a/test.log b/test.log
index 63f5b542..77981c86 100644
--- a/test.log
+++ b/test.log
@@ -1,15 +1,24 @@
Loading mkin
Testing mkin
✔ | OK F W S | Context
- ⠏ | 0 | Export dataset for reading into CAKE ⠋ | 1 | Export dataset for reading into CAKE ⠙ | 1 1 | Export dataset for reading into CAKE ⠙ | 2 | Export dataset for reading into CAKE ⠹ | 3 | Export dataset for reading into CAKE ⠸ | 4 | Export dataset for reading into CAKE ⠼ | 5 | Export dataset for reading into CAKE ⠴ | 6 | Export dataset for reading into CAKE ⠦ | 7 | Export dataset for reading into CAKE ⠧ | 8 | Export dataset for reading into CAKE ⠇ | 8 1 | Export dataset for reading into CAKE ✔ | 8 1 | Export dataset for reading into CAKE [1.4 s]
-────────────────────────────────────────────────────────────────────────────────
-test_CAKE_export.R:50: skip: Test data from Appendix D are correctly evaluated
-Figure not generated yet: plot-nafta-analysis.svg
-Please run `vdiffr::manage_cases()` to validate the figure.
-────────────────────────────────────────────────────────────────────────────────
- ⠏ | 0 | Calculation of FOCUS chi2 error levels ⠋ | 1 | Calculation of FOCUS chi2 error levels ⠙ | 2 | Calculation of FOCUS chi2 error levels ✔ | 2 | Calculation of FOCUS chi2 error levels [2.2 s]
- ⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠼ | 5 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠴ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠦ | 7 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠧ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠇ | 9 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠏ | 10 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 11 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 12 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [7.8 s]
- ⠏ | 0 | Iteratively reweighted least squares (IRLS) fitting ⠋ | 1 | Iteratively reweighted least squares (IRLS) fitting ⠙ | 2 | Iteratively reweighted least squares (IRLS) fitting ⠹ | 2 1 | Iteratively reweighted least squares (IRLS) fitting ✔ | 2 1 | Iteratively reweighted least squares (IRLS) fitting [15.9 s]
+ ⠏ | 0 | Export dataset for reading into CAKE ⠋ | 1 | Export dataset for reading into CAKE ⠙ | 1 1 | Export dataset for reading into CAKE ✖ | 1 1 | Export dataset for reading into CAKE
+────────────────────────────────────────────────────────────────────────────────
+test_CAKE_export.R:32: error: Test data from Appendix D are correctly evaluated
+Objekt 'MRID_555555' nicht gefunden
+1: expect_message(res <- nafta(MRID_555555, "MRID 555555")) at /home/jranke/git/mkin/tests/testthat/test_CAKE_export.R:32
+2: quasi_capture(enquo(object), capture_messages, label = label)
+3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
+4: withCallingHandlers(code, message = function(condition) {
+ out$push(condition)
+ invokeRestart("muffleMessage")
+ })
+5: eval_bare(get_expr(quo), get_env(quo))
+6: nafta(MRID_555555, "MRID 555555")
+7: levels(ds$name) at /home/jranke/git/mkin/R/nafta.R:20
+────────────────────────────────────────────────────────────────────────────────
+ ⠏ | 0 | Calculation of FOCUS chi2 error levels ⠋ | 1 | Calculation of FOCUS chi2 error levels ⠙ | 2 | Calculation of FOCUS chi2 error levels ✔ | 2 | Calculation of FOCUS chi2 error levels [2.3 s]
+ ⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠼ | 5 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠴ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠦ | 7 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠧ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠇ | 9 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠏ | 10 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 11 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 12 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠸ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [7.9 s]
+ ⠏ | 0 | Iteratively reweighted least squares (IRLS) fitting ⠋ | 1 | Iteratively reweighted least squares (IRLS) fitting ⠙ | 2 | Iteratively reweighted least squares (IRLS) fitting ⠹ | 2 1 | Iteratively reweighted least squares (IRLS) fitting ✔ | 2 1 | Iteratively reweighted least squares (IRLS) fitting [16.0 s]
────────────────────────────────────────────────────────────────────────────────
test_irls.R:48: skip: Reweighting method 'tc' works
Too much trouble with datasets that are randomly generated
@@ -20,9 +29,9 @@ 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 2015 NAFTA guidance ⠋ | 1 | Evaluations according to 2015 NAFTA guidance ⠙ | 1 1 | Evaluations according to 2015 NAFTA guidance ⠙ | 2 | Evaluations according to 2015 NAFTA guidance ⠹ | 3 | Evaluations according to 2015 NAFTA guidance ⠸ | 4 | Evaluations according to 2015 NAFTA guidance ⠼ | 5 | Evaluations according to 2015 NAFTA guidance ⠴ | 6 | Evaluations according to 2015 NAFTA guidance ⠦ | 7 | Evaluations according to 2015 NAFTA guidance ⠧ | 8 | Evaluations according to 2015 NAFTA guidance ⠇ | 9 | Evaluations according to 2015 NAFTA guidance ✔ | 9 | Evaluations according to 2015 NAFTA guidance [0.8 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 [23.7 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 | Evaluations according to 2015 NAFTA guidance ⠋ | 1 | Evaluations according to 2015 NAFTA guidance ⠙ | 2 | Evaluations according to 2015 NAFTA guidance ⠹ | 3 | Evaluations according to 2015 NAFTA guidance ⠸ | 4 | Evaluations according to 2015 NAFTA guidance ⠼ | 5 | Evaluations according to 2015 NAFTA guidance ⠴ | 6 | Evaluations according to 2015 NAFTA guidance ⠦ | 7 | Evaluations according to 2015 NAFTA guidance ⠧ | 8 | Evaluations according to 2015 NAFTA guidance ⠇ | 9 | Evaluations according to 2015 NAFTA guidance ⠏ | 9 1 | Evaluations according to 2015 NAFTA guidance ⠏ | 10 | Evaluations according to 2015 NAFTA guidance ⠋ | 11 | Evaluations according to 2015 NAFTA guidance ⠙ | 12 | Evaluations according to 2015 NAFTA guidance ⠹ | 13 | Evaluations according to 2015 NAFTA guidance ⠸ | 14 | Evaluations according to 2015 NAFTA guidance ⠼ | 15 | Evaluations according to 2015 NAFTA guidance ⠴ | 16 | Evaluations according to 2015 NAFTA guidance ⠦ | 17 | Evaluations according to 2015 NAFTA guidance ✔ | 17 | Evaluations according to 2015 NAFTA guidance [1.5 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 [24.5 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) [7.3 s]
⠏ | 0 | Summary ⠋ | 1 | Summary ✔ | 1 | Summary
⠏ | 0 | Plotting ⠋ | 1 | Plotting ⠙ | 1 1 | Plotting ⠹ | 2 1 | Plotting ⠸ | 3 1 | Plotting ✔ | 3 1 | Plotting [0.3 s]
────────────────────────────────────────────────────────────────────────────────
@@ -31,12 +40,12 @@ Figure not generated yet: mkinparplot-for-focus-c-sfo.svg
Please run `vdiffr::manage_cases()` to validate the figure.
────────────────────────────────────────────────────────────────────────────────
⠏ | 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) [7.3 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]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 74.6 s
+Duration: 75.2 s
-OK: 77
-Failed: 0
+OK: 79
+Failed: 1
Warnings: 0
-Skipped: 4
+Skipped: 3
diff --git a/tests/figs/evaluations-according-to-2015-nafta-guidance/nafta-sop-appendix-b.svg b/tests/figs/evaluations-according-to-2015-nafta-guidance/nafta-sop-appendix-b.svg
new file mode 100644
index 00000000..617e39b3
--- /dev/null
+++ b/tests/figs/evaluations-according-to-2015-nafta-guidance/nafta-sop-appendix-b.svg
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diff --git a/tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg b/tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg
new file mode 100644
index 00000000..c6a19428
--- /dev/null
+++ b/tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg
@@ -0,0 +1,85 @@
+<?xml version='1.0' encoding='UTF-8' ?>
+<svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' viewBox='0 0 720.00 576.00'>
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+ line, polyline, polygon, path, rect, circle {
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+ stroke-linecap: round;
+ stroke-linejoin: round;
+ stroke-miterlimit: 10.00;
+ }
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diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index d695e90d..22c5f2b4 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: 2019-02-25
+Date: 2019-02-26
Optimiser: IRLS
[Data]
diff --git a/tests/testthat/NAFTA_SOP_Appendix_B.txt b/tests/testthat/NAFTA_SOP_Appendix_B.txt
new file mode 100644
index 00000000..54b70880
--- /dev/null
+++ b/tests/testthat/NAFTA_SOP_Appendix_B.txt
@@ -0,0 +1,35 @@
+Sums of squares:
+ SFO IORE DFOP
+174.39718 21.91831 16.57180
+
+Critical sum of squares for checking the SFO model:
+[1] 26.93798
+
+Parameters:
+$SFO
+ Estimate Pr(>t) Lower Upper
+parent_0 51.2430312 1.178492e-10 45.4036817 57.0823806
+k_parent_sink 0.2531291 1.608492e-06 0.1935733 0.3310082
+
+$IORE
+ Estimate Pr(>t) Lower Upper
+parent_0 51.71052958 8.522722e-15 4.951371e+01 53.907348315
+k__iore_parent_sink 0.00134836 6.841092e-02 3.421381e-04 0.005313861
+N_parent 2.66146927 3.975823e-08 2.191012e+00 3.131926902
+
+$DFOP
+ Estimate Pr(>t) Lower Upper
+parent_0 51.70546719 3.457982e-14 49.677926850 53.73300753
+k1 0.41569648 1.002119e-06 0.330769606 0.52242879
+k2 0.01273299 1.393989e-03 0.007230162 0.02242399
+g 0.83380396 5.718367e-12 0.771816175 0.88153694
+
+
+DTx values:
+ DT50 DT90 DT50_rep
+SFO 3 9 3
+IORE 1 28 9
+DFOP 2 40 54
+
+Representative half-life:
+[1] 8.573301
diff --git a/tests/testthat/print_nafta_analysis.txt b/tests/testthat/NAFTA_SOP_Appendix_D.txt
index 61d2539f..d01accf2 100644
--- a/tests/testthat/print_nafta_analysis.txt
+++ b/tests/testthat/NAFTA_SOP_Appendix_D.txt
@@ -1,6 +1,8 @@
Sums of squares:
SFO IORE DFOP
1378.6832 615.7730 517.8836
+
+Critical sum of squares for checking the SFO model:
[1] 717.4598
Parameters:
diff --git a/tests/testthat/test_CAKE_export.R b/tests/testthat/test_CAKE_export.R
index aeb192c8..5f984782 100644
--- a/tests/testthat/test_CAKE_export.R
+++ b/tests/testthat/test_CAKE_export.R
@@ -27,25 +27,3 @@ test_that("Exporting is reproducible", {
csf <- readLines(con = "FOCUS_2006_D.csf")
expect_known_output(csf, "FOCUS_2006_D.txt")
})
-
-test_that("Test data from Appendix D are correctly evaluated", {
- expect_message(res <- nafta(MRID_555555, "MRID 555555"))
-
- # From Figure D.1
- dtx_sop <- matrix(c(407, 541, 429, 1352, 5192066, 2383), nrow = 3, ncol = 2)
- expect_equivalent(res$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$parameters, function(x) x["parent_0", "Estimate"])
- expect_equivalent(C0_mkin, C0_sop, scale = 1, tolerance = 0.1)
-
- expect_equal(round(res$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", plot_nafta)
-})
diff --git a/tests/testthat/test_nafta.R b/tests/testthat/test_nafta.R
index 10de3ce0..a50d8f36 100644
--- a/tests/testthat/test_nafta.R
+++ b/tests/testthat/test_nafta.R
@@ -21,13 +21,33 @@ context("Evaluations according to 2015 NAFTA guidance")
test_that("Data for more than one compound are rejected",
expect_error(nafta(FOCUS_2006_D)))
+test_that("Test data from Appendix B are correctly evaluated", {
+ expect_message(res <- nafta(NAFTA_SOP_Appendix_B, "aerobic aquatic"))
+
+ # From Figure D.1
+ dtx_sop <- matrix(c(2.74, 1.37, 2.17, 9.1, 28.5, 39.9), nrow = 3, ncol = 2)
+ expect_equivalent(signif(res$distimes[, 1:2], 3), dtx_sop)
+
+ C0_sop <- c(SFO = 51.2, IORE = 51.7, DFOP = 51.7)
+ C0_mkin <- sapply(res$parameters, function(x) x["parent_0", "Estimate"])
+ expect_equivalent(C0_mkin, C0_sop, scale = 1, tolerance = 0.1)
+
+ expect_equal(signif(res$S_c, 3), 26.9)
+ expect_equal(signif(res$S[["SFO"]], 3), 174)
+ expect_equal(signif(res$t_rep, 3), 8.57)
+
+ expect_known_output(print(res), "NAFTA_SOP_Appendix_B.txt")
+
+ plot_nafta <- function() plot(res)
+ vdiffr::expect_doppelganger("NAFTA SOP Appendix B", plot_nafta)
+})
+
test_that("Test data from Appendix D are correctly evaluated", {
- expect_message(res <- nafta(MRID_555555, "MRID 555555"))
+ expect_message(res <- nafta(NAFTA_SOP_Appendix_D, "MRID 555555"))
# From Figure D.1
dtx_sop <- matrix(c(407, 541, 429, 1352, 5192066, 2383), nrow = 3, ncol = 2)
- expect_equivalent(res$distimes[, 1:2], dtx_sop, tolerance = 1,
- scale = 1)
+ expect_equivalent(round(res$distimes[, 1:2]), dtx_sop)
C0_sop <- c(SFO = 83.8, IORE = 96.9, DFOP = 97.6)
C0_mkin <- sapply(res$parameters, function(x) x["parent_0", "Estimate"])
@@ -37,7 +57,7 @@ test_that("Test data from Appendix D are correctly evaluated", {
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")
+ expect_known_output(print(res), "NAFTA_SOP_Appendix_D.txt")
plot_nafta <- function() plot(res)
vdiffr::expect_doppelganger("Plot NAFTA analysis", plot_nafta)

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