diff options
| -rw-r--r-- | test.log | 20 | ||||
| -rw-r--r-- | tests/testthat/FOCUS_2006_D.csf | 2 | ||||
| -rw-r--r-- | tests/testthat/test_nlme.R | 27 |
3 files changed, 37 insertions, 12 deletions
@@ -6,30 +6,30 @@ Testing mkin ✔ | 4 | Calculation of FOCUS chi2 error levels [2.2 s] ✔ | 4 | Fitting the SFORB model [1.7 s] ✔ | 5 | Calculation of Akaike weights -✔ | 10 | Confidence intervals and p-values [9.5 s] -✔ | 14 | Error model fitting [38.0 s] +✔ | 10 | Confidence intervals and p-values [9.4 s] +✔ | 14 | Error model fitting [38.1 s] ✔ | 6 | Test fitting the decline of metabolites from their maximum [0.8 s] ✔ | 1 | Fitting the logistic model [0.9 s] ✔ | 1 | Test dataset class mkinds used in gmkin ✔ | 12 | Special cases of mkinfit calls [2.3 s] ✔ | 9 | mkinmod model generation and printing [0.2 s] -✔ | 3 | Model predictions with mkinpredict [0.3 s] +✔ | 3 | Model predictions with mkinpredict [0.4 s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.1 s] -✔ | 5 | Nonlinear mixed-effects models [11.1 s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3 s] +✔ | 8 | Nonlinear mixed-effects models [11.9 s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s] ✔ | 3 | Summary -✔ | 14 | Plotting [4.8 s] +✔ | 14 | Plotting [4.9 s] ✔ | 4 | AIC calculation ✔ | 4 | Residuals extracted from mkinfit models ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s] ✔ | 1 | Summaries of old mkinfit objects -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [6.9 s] -✔ | 9 | Hypothesis tests [36.8 s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.1 s] +✔ | 9 | Hypothesis tests [36.9 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 130.9 s +Duration: 132.2 s -OK: 150 +OK: 153 Failed: 0 Warnings: 0 Skipped: 0 diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf index de5ee0a4..dfccc13f 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: 2020-04-09 +Date: 2020-04-16 Optimiser: IRLS [Data] diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R index efbc231a..d272af38 100644 --- a/tests/testthat/test_nlme.R +++ b/tests/testthat/test_nlme.R @@ -1,5 +1,7 @@ context("Nonlinear mixed-effects models") +library(nlme) + test_that("nlme_function works correctly", { sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) @@ -47,8 +49,27 @@ test_that("nlme_function works correctly", { expect_equal(m_nlme_raw$coefficients, m_nlme_mkin$coefficients) + m_nlme_mmkin <- nlme(f) + + m_nlme_raw_2 <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink), + data = grouped_data, + fixed = parent_0 + log_k_parent_sink ~ 1, + random = pdDiag(parent_0 + log_k_parent_sink ~ 1), + start = mean_degparms(f, random = TRUE)) + + expect_equal(m_nlme_raw_2$coefficients, m_nlme_mmkin$coefficients) + + anova_nlme <- anova(m_nlme_mmkin, m_nlme_raw) # mmkin needs to go first as we had + # to adapt the method due to + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17761 + + # We get a slightly lower AIC with the improved starting values used within + # nlme.mmkin + expect_lt(anova_nlme["m_nlme_mmkin", "AIC"], + anova_nlme["m_nlme_raw", "AIC"]) + m_nlme_raw_up_1 <- update(m_nlme_raw, random = log_k_parent_sink ~ 1) - # The following two calls give an error although they should + # The following three calls give an error although they should # do the same as the call above # The error occurs in the evaluation of the modelExpression in the # call to .C(fit_nlme, ...) @@ -58,16 +79,20 @@ test_that("nlme_function works correctly", { # fixed = parent_0 + log_k_parent_sink ~ 1, # random = log_k_parent_sink ~ 1, # start = mean_dp) + # update(m_nlme_mmkin, random = pdDiag(log_k_parent_sink ~ 1), + # start = c(parent_0 = 100, log_k_parent_sink = 0.1)) m_nlme_raw_up_2 <- update(m_nlme_raw, random = parent_0 ~ 1) m_nlme_mkin_up_2 <- update(m_nlme_mkin, random = parent_0 ~ 1) expect_equal(m_nlme_raw_up_2$coefficients, m_nlme_mkin_up_2$coefficients) expect_silent(tmp <- update(m_nlme_mkin)) + expect_silent(tmp <- update(m_nlme_mmkin)) }) test_that("nlme_function works correctly in other cases", { + skip_on_cran() dt50_in <- c(400, 800, 1200, 1600, 2000) k_in <- log(2) / dt50_in SFO <- mkinmod(parent = mkinsub("SFO")) |