diff options
| -rw-r--r-- | R/tffm0.R | 19 | ||||
| -rw-r--r-- | man/tffm0.Rd | 20 | ||||
| -rw-r--r-- | test.log | 15 | ||||
| -rw-r--r-- | tests/testthat/test_tffm0.R | 10 |
4 files changed, 41 insertions, 23 deletions
@@ -1,15 +1,18 @@ #' Transform formation fractions as in the first published mkin version #' -#' The transformed fractions can be restricted between 0 and 1 in model -#' optimisations. Therefore this transformation was used originally in mkin. It -#' was later replaced by the [ilr] transformation because the ilr transformed +#' This transformation was used originally in mkin, in order to implement a +#' constraint for the sum of formation fractions to be smaller than 1. It was +#' later replaced by the [ilr] transformation because the ilr transformed #' fractions can assumed to follow normal distribution. As the ilr #' transformation is not available in [RxODE] and can therefore not be used in -#' the nlmixr modelling language, this transformation is currently used for -#' translating mkin models with formation fractions to more than one target -#' compartment for fitting with nlmixr in [nlmixr_model]. However, -#' this implementation cannot be used there, as it is not accessible -#' from RxODE. +#' the nlmixr modelling language, the original transformation is currently used +#' for translating mkin models with formation fractions to more than one target +#' compartment for fitting with nlmixr in [nlmixr_model]. However, this +#' implementation cannot be used there, as it is not accessible from RxODE. +#' +#' If the transformed formation fractions are restricted to the interval +#' between 0 and 1, the sum of backtransformed values is restricted +#' to this interval. #' #' @param ff Vector of untransformed formation fractions. The sum #' must be smaller or equal to one diff --git a/man/tffm0.Rd b/man/tffm0.Rd index 46978d5e..89bee7d9 100644 --- a/man/tffm0.Rd +++ b/man/tffm0.Rd @@ -22,16 +22,20 @@ A vector of the transformed formation fractions A vector of backtransformed formation fractions for natural use in degradation models } \description{ -The transformed fractions can be restricted between 0 and 1 in model -optimisations. Therefore this transformation was used originally in mkin. It -was later replaced by the \link{ilr} transformation because the ilr transformed +This transformation was used originally in mkin, in order to implement a +constraint for the sum of formation fractions to be smaller than 1. It was +later replaced by the \link{ilr} transformation because the ilr transformed fractions can assumed to follow normal distribution. As the ilr transformation is not available in \link{RxODE} and can therefore not be used in -the nlmixr modelling language, this transformation is currently used for -translating mkin models with formation fractions to more than one target -compartment for fitting with nlmixr in \link{nlmixr_model}. However, -this implementation cannot be used there, as it is not accessible -from RxODE. +the nlmixr modelling language, the original transformation is currently used +for translating mkin models with formation fractions to more than one target +compartment for fitting with nlmixr in \link{nlmixr_model}. However, this +implementation cannot be used there, as it is not accessible from RxODE. +} +\details{ +If the transformed formation fractions are restricted to the interval +between 0 and 1, the sum of backtransformed values is restricted +to this interval. } \examples{ ff_example <- c( @@ -8,19 +8,19 @@ Loading required package: parallel ✔ | 2 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.0s] ⠋ | 1 | Dimethenamid data from 2018 -✔ | 1 25 | Dimethenamid data from 2018 [49.4s] +✔ | 1 25 | Dimethenamid data from 2018 [52.3s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_dmta.R:147:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data Reason: Fitting this ODE model with saemix takes about 15 minutes on my system ──────────────────────────────────────────────────────────────────────────────── -✔ | 14 | Error model fitting [6.9s] +✔ | 14 | Error model fitting [7.1s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.8s] ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.2s] ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.6s] ✔ | 1 | Fitting the logistic model [0.4s] ⠴ | 6 | Nonlinear mixed-effects models -✔ | 1 15 | Nonlinear mixed-effects models [2.4s] +✔ | 1 15 | Nonlinear mixed-effects models [2.5s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_mixed.R:67:3): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve @@ -30,24 +30,25 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve ✔ | 3 | mkinfit features [1.1s] ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.1s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.2s] ✔ | 9 | Nonlinear mixed-effects models with nlme [9.2s] ✔ | 16 | Plotting [1.5s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 23 | saemix_parent [29.2s] +✔ | 23 | saemix_parent [29.1s] ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6s] ✔ | 7 | Fitting the SFORB model [4.4s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 4 | Summary [0.1s] ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.6s] ✔ | 9 | Hypothesis tests [9.4s] +✔ | 2 | tffm0 ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 132.0 s +Duration: 135.1 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) • Fitting with saemix takes around 10 minutes when using deSolve (1) -[ FAIL 0 | WARN 0 | SKIP 2 | PASS 237 ] +[ FAIL 0 | WARN 0 | SKIP 2 | PASS 239 ] diff --git a/tests/testthat/test_tffm0.R b/tests/testthat/test_tffm0.R new file mode 100644 index 00000000..82e1ee94 --- /dev/null +++ b/tests/testthat/test_tffm0.R @@ -0,0 +1,10 @@ +test_that("The formation fraction transformation tffm0 is reversible", { + ff_example <- c( + 0.10983681, 0.09035905, 0.08399383 + ) + ff_example_trans <- tffm0(ff_example) + expect_equal(invtffm0(ff_example_trans), ff_example) + + ff_ex_2_trans <- c(0.5, 0.9, 0.99) + expect_true(sum(invtffm0(ff_ex_2_trans)) < 1) +}) |