diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-02-26 09:12:50 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-02-26 09:12:50 +0100 |
| commit | 6693ee373c61d716e877386d6be16e3f9f0f40ab (patch) | |
| tree | 7e1e8607c96b459878ca81e9b183795399aeb516 | |
| parent | 885ea2cd3392e57efff72e5094643917d6ba2be8 (diff) | |
Add another NAFTA dataset + test
| -rw-r--r-- | R/nafta.R | 3 | ||||
| -rw-r--r-- | build.log | 1 | ||||
| -rw-r--r-- | data/NAFTA_2015.rda | bin | 264 -> 0 bytes | |||
| -rw-r--r-- | data/NAFTA_SOP_2015.rda | bin | 0 -> 390 bytes | |||
| -rw-r--r-- | man/NAFTA_SOP_2015.Rd (renamed from man/NAFTA_2015_datasets.Rd) | 15 | ||||
| -rw-r--r-- | man/nafta.Rd | 2 | ||||
| -rw-r--r-- | test.log | 43 | ||||
| -rw-r--r-- | tests/figs/evaluations-according-to-2015-nafta-guidance/nafta-sop-appendix-b.svg | 462 | ||||
| -rw-r--r-- | tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg | 85 | ||||
| -rw-r--r-- | tests/testthat/FOCUS_2006_D.csf | 2 | ||||
| -rw-r--r-- | tests/testthat/NAFTA_SOP_Appendix_B.txt | 35 | ||||
| -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.R | 22 | ||||
| -rw-r--r-- | tests/testthat/test_nafta.R | 28 |
14 files changed, 647 insertions, 53 deletions
@@ -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) @@ -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 Binary files differdeleted file mode 100644 index 48183048..00000000 --- a/data/NAFTA_2015.rda +++ /dev/null diff --git a/data/NAFTA_SOP_2015.rda b/data/NAFTA_SOP_2015.rda Binary files differnew file mode 100644 index 00000000..eb7ce63f --- /dev/null +++ b/data/NAFTA_SOP_2015.rda 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) } @@ -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 @@ -0,0 +1,462 @@ +<?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'> +<defs> + <style type='text/css'><![CDATA[ + line, polyline, polygon, path, rect, circle { + fill: none; + stroke: #000000; + stroke-linecap: round; + stroke-linejoin: round; + stroke-miterlimit: 10.00; + } + ]]></style> 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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) |
