diff options
| -rw-r--r-- | tests/testthat/test_FOCUS_D_UBA_expertise.R | 48 |
1 files changed, 34 insertions, 14 deletions
diff --git a/tests/testthat/test_FOCUS_D_UBA_expertise.R b/tests/testthat/test_FOCUS_D_UBA_expertise.R index 3b241aa4..74097afa 100644 --- a/tests/testthat/test_FOCUS_D_UBA_expertise.R +++ b/tests/testthat/test_FOCUS_D_UBA_expertise.R @@ -19,15 +19,19 @@ context("Results for FOCUS D established in expertise for UBA (Ranke 2014)") # Results are from p. 40 +SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"), + m1 = list(type = "SFO"), quiet = TRUE) +SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"), + m1 = list(type = "SFO"), + use_of_ff = "max", quiet = TRUE) + test_that("Fits without formation fractions are correct for FOCUS D", { - SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO"), quiet = TRUE) fit.default <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) - expect_equal(round(as.numeric(endpoints(fit.default)$distimes["parent", ]), 2), + expect_equal(round(as.numeric(endpoints(fit.default)$distimes["parent", ]), 2), c(7.02, 23.33)) - expect_equal(round(as.numeric(endpoints(fit.default)$distimes["m1", ]), 1), + expect_equal(round(as.numeric(endpoints(fit.default)$distimes["m1", ]), 1), c(131.8, 437.7)) expect_equal(signif(summary(fit.default)$bpar[, "t value"], 5), @@ -36,20 +40,36 @@ test_that("Fits without formation fractions are correct for FOCUS D", { test_that("Fits with formation fractions are correct for FOCUS D", { skip_on_cran() - SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO"), - use_of_ff = "max", quiet = TRUE) - fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) - expect_equivalent(round(fit.ff$bparms.optim, c(2, 4, 4, 4)), + expect_equivalent(round(fit.ff$bparms.optim, c(2, 4, 4, 4)), c(99.60, 0.0987, 0.0053, 0.5145)) - expect_equivalent(round(100 * mkinerrmin(fit.ff)$err.min, 2), + expect_equivalent(round(100 * mkinerrmin(fit.ff)$err.min, 2), c(6.40, 6.46, 4.69)) - expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["parent", ]), 2), + expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["parent", ]), 2), + c(7.02, 23.33)) + expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["m1", ]), 1), + c(131.8, 437.7)) +}) + +test_that("Fits without internal transformations are correct for FOCUS D", { + skip_on_cran() + expect_warning( + fit.ff.notrans <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, + transform_fractions = FALSE, transform_rates = FALSE, quiet = TRUE), + "sum of formation fractions") + + expect_equivalent(round(fit.ff.notrans$bparms.optim, c(2, 4, 4, 4)), + c(99.60, 0.0987, 0.0053, 0.5145)) + + expect_equivalent(round(100 * mkinerrmin(fit.ff.notrans)$err.min, 2), + c(6.40, 6.46, 4.69)) + + + expect_equal(round(as.numeric(endpoints(fit.ff.notrans)$distimes["parent", ]), 2), c(7.02, 23.33)) - expect_equal(round(as.numeric(endpoints(fit.ff)$distimes["m1", ]), 1), + expect_equal(round(as.numeric(endpoints(fit.ff.notrans)$distimes["m1", ]), 1), c(131.8, 437.7)) }) @@ -64,13 +84,13 @@ test_that("The t-value for fits using internal transformations corresponds with M2 = mkinsub("SFO"), use_of_ff = "min", quiet = TRUE) - fit_DFOP_par_c_2 <- mkinfit(m_synth_DFOP_par.minff, + fit_DFOP_par_c_2 <- mkinfit(m_synth_DFOP_par.minff, synthetic_data_for_UBA_2014[[12]]$data, quiet = TRUE) # Note that the k1 and k2 are exchanged in the untransformed fit evaluated with FME for this test expect_equal(signif(summary(fit_DFOP_par_c_2)$bpar[1:7, "t value"], 5), - c(parent_0 = 80.054, k_M1_sink = 12.291, k_M2_sink = 10.588, + c(parent_0 = 80.054, k_M1_sink = 12.291, k_M2_sink = 10.588, f_parent_to_M1 = 21.4960, f_parent_to_M2 = 24.0890, k1 = 16.1450, k2 = 8.1747)) }) |