From 609bfe2fd7ecbdcad5f5d641f0db51541dcd6a4e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 28 May 2020 12:24:32 +0200 Subject: use_of_ff = "max" for shorthand models like "SFO" --- NEWS.md | 2 ++ R/mkinfit.R | 2 +- test.log | 14 +++++++------- tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg | 2 +- tests/testthat/FOCUS_2006_D.csf | 2 +- tests/testthat/NAFTA_SOP_Appendix_B.txt | 18 +++++++++--------- tests/testthat/NAFTA_SOP_Appendix_D.txt | 18 +++++++++--------- tests/testthat/test_confidence.R | 4 ++-- tests/testthat/test_nlme.R | 6 +++--- 9 files changed, 35 insertions(+), 33 deletions(-) diff --git a/NEWS.md b/NEWS.md index 8f88b64d..0d5c93d3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -8,6 +8,8 @@ - 'confint(method = 'profile'): Choose accuracy based on 'rel_tol' argument, relative to the bounds obtained by the quadratic approximation +- 'mkinfit': Make 'use_of_ff' = "max" also the default for models specified using short names like "SFO" or "FOMC" + # mkin 0.9.50.2 (2020-05-12) - Increase tolerance for a platform specific test results on the Solaris test machine on CRAN diff --git a/R/mkinfit.R b/R/mkinfit.R index 393473d1..f9cb3304 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -268,7 +268,7 @@ mkinfit <- function(mkinmod, observed, if (mkinmod[[1]] %in% parent_models_available) { speclist <- list(list(type = mkinmod, sink = TRUE)) names(speclist) <- presumed_parent_name - mkinmod <- mkinmod(speclist = speclist, use_of_ff = "min") + mkinmod <- mkinmod(speclist = speclist, use_of_ff = "max") } else { stop("Argument mkinmod must be of class mkinmod or a string containing one of\n ", paste(parent_models_available, collapse = ", ")) diff --git a/test.log b/test.log index 3dcf271d..e026e559 100644 --- a/test.log +++ b/test.log @@ -7,28 +7,28 @@ Testing mkin ✔ | 7 | Fitting the SFORB model [3.3 s] ✔ | 5 | Analytical solutions for coupled models [3.1 s] ✔ | 5 | Calculation of Akaike weights -✔ | 10 | Confidence intervals and p-values [1.0 s] -✔ | 14 | Error model fitting [3.9 s] +✔ | 10 | Confidence intervals and p-values [1.1 s] +✔ | 14 | Error model fitting [4.0 s] ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s] ✔ | 1 | Fitting the logistic model [0.2 s] ✔ | 1 | Test dataset class mkinds used in gmkin ✔ | 12 | Special cases of mkinfit calls [0.6 s] ✔ | 8 | mkinmod model generation and printing [0.2 s] ✔ | 3 | Model predictions with mkinpredict [0.4 s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5 s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6 s] ✔ | 9 | Nonlinear mixed-effects models [7.7 s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s] -✔ | 3 | Summary [0.1 s] -✔ | 14 | Plotting [1.4 s] +✔ | 3 | Summary +✔ | 14 | Plotting [1.5 s] ✔ | 4 | AIC calculation ✔ | 4 | Residuals extracted from mkinfit models ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4 s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s] -✔ | 9 | Hypothesis tests [6.5 s] +✔ | 9 | Hypothesis tests [6.6 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 38.2 s +Duration: 38.5 s OK: 159 Failed: 0 diff --git a/tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg b/tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg index ab517c96..62590397 100644 --- a/tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg +++ b/tests/figs/plotting/mkinparplot-for-focus-c-sfo.svg @@ -73,7 +73,7 @@ -k_parent_sink +k_parent diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf index 5d946ecd..f845cc1d 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: 2020-05-26 +Date: 2020-05-28 Optimiser: IRLS [Data] diff --git a/tests/testthat/NAFTA_SOP_Appendix_B.txt b/tests/testthat/NAFTA_SOP_Appendix_B.txt index 294ea09f..2a23f5da 100644 --- a/tests/testthat/NAFTA_SOP_Appendix_B.txt +++ b/tests/testthat/NAFTA_SOP_Appendix_B.txt @@ -7,17 +7,17 @@ Critical sum of squares for checking the SFO model: Parameters: $SFO - Estimate Pr(>t) Lower Upper -parent_0 51.243 2.12e-10 45.724 56.762 -k_parent_sink 0.253 2.95e-06 0.193 0.332 -sigma 3.529 1.28e-04 2.061 4.997 + Estimate Pr(>t) Lower Upper +parent_0 51.243 2.12e-10 45.724 56.762 +k_parent 0.253 2.95e-06 0.193 0.332 +sigma 3.529 1.28e-04 2.061 4.997 $IORE - Estimate Pr(>t) Lower Upper -parent_0 51.71053 2.60e-14 4.97e+01 53.68122 -k__iore_parent_sink 0.00135 5.21e-02 3.88e-04 0.00469 -N_parent 2.66147 3.67e-08 2.23e+00 3.08855 -sigma 1.25124 1.76e-04 7.24e-01 1.77811 + Estimate Pr(>t) Lower Upper +parent_0 51.71053 2.60e-14 4.97e+01 53.68122 +k__iore_parent 0.00135 5.21e-02 3.88e-04 0.00469 +N_parent 2.66147 3.67e-08 2.23e+00 3.08855 +sigma 1.25124 1.76e-04 7.24e-01 1.77811 $DFOP Estimate Pr(>t) Lower Upper diff --git a/tests/testthat/NAFTA_SOP_Appendix_D.txt b/tests/testthat/NAFTA_SOP_Appendix_D.txt index 375830b7..c0b7035c 100644 --- a/tests/testthat/NAFTA_SOP_Appendix_D.txt +++ b/tests/testthat/NAFTA_SOP_Appendix_D.txt @@ -7,17 +7,17 @@ Critical sum of squares for checking the SFO model: Parameters: $SFO - Estimate Pr(>t) Lower Upper -parent_0 83.7558 1.80e-14 77.18268 90.3288 -k_parent_sink 0.0017 7.43e-05 0.00112 0.0026 -sigma 8.7518 1.22e-05 5.64278 11.8608 + Estimate Pr(>t) Lower Upper +parent_0 83.7558 1.80e-14 77.18268 90.3288 +k_parent 0.0017 7.43e-05 0.00112 0.0026 +sigma 8.7518 1.22e-05 5.64278 11.8608 $IORE - Estimate Pr(>t) Lower Upper -parent_0 9.69e+01 NA 8.88e+01 1.05e+02 -k__iore_parent_sink 8.40e-14 NA 1.79e-18 3.94e-09 -N_parent 6.68e+00 NA 4.19e+00 9.17e+00 -sigma 5.85e+00 NA 3.76e+00 7.94e+00 + Estimate Pr(>t) Lower Upper +parent_0 9.69e+01 NA 8.88e+01 1.05e+02 +k__iore_parent 8.40e-14 NA 1.79e-18 3.94e-09 +N_parent 6.68e+00 NA 4.19e+00 9.17e+00 +sigma 5.85e+00 NA 3.76e+00 7.94e+00 $DFOP Estimate Pr(>t) Lower Upper diff --git a/tests/testthat/test_confidence.R b/tests/testthat/test_confidence.R index e85fdb7a..3fdd3f2c 100644 --- a/tests/testthat/test_confidence.R +++ b/tests/testthat/test_confidence.R @@ -67,9 +67,9 @@ test_that("Likelihood profile based confidence intervals work", { f <- fits[["SFO", "FOCUS_C"]] # negative log-likelihood for use with mle - f_nll <- function(parent_0, k_parent_sink, sigma) { + f_nll <- function(parent_0, k_parent, sigma) { - f$ll(c(parent_0 = as.numeric(parent_0), - k_parent_sink = as.numeric(k_parent_sink), + k_parent = as.numeric(k_parent), sigma = as.numeric(sigma))) } f_mle <- stats4::mle(f_nll, start = as.list(parms(f)), nobs = nrow(FOCUS_2006_C)) diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R index 31fb19de..5a8db142 100644 --- a/tests/testthat/test_nlme.R +++ b/tests/testthat/test_nlme.R @@ -51,10 +51,10 @@ test_that("nlme_function works correctly", { m_nlme_mmkin <- nlme(f) - m_nlme_raw_2 <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink), + m_nlme_raw_2 <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent), data = grouped_data, - fixed = parent_0 + log_k_parent_sink ~ 1, - random = pdDiag(parent_0 + log_k_parent_sink ~ 1), + fixed = parent_0 + log_k_parent ~ 1, + random = pdDiag(parent_0 + log_k_parent ~ 1), start = mean_degparms(f, random = TRUE)) expect_equal(m_nlme_raw_2$coefficients, m_nlme_mmkin$coefficients) -- cgit v1.2.1