Add another NAFTA dataset + test

7 files changed, 609 insertions, 27 deletions

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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+<polyline points='665.33,421.20 665.33,417.60 665.33,414.00 ' style='stroke-width: 0.75;' clip-path='url(#cpMzAuMjR8Njg5Ljc2fDU0NS43NnwyODkuNDQ=)' />
+<defs>
+  <clipPath id='cpNTkuMDR8Njg5Ljc2fDUwMi41Nnw1OS4wNA=='>
+    <rect x='59.04' y='59.04' width='630.72' height='443.52' />
+  </clipPath>
+</defs>
+</svg>
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)