diff options
| -rw-r--r-- | NEWS.md | 2 | ||||
| -rw-r--r-- | R/saem.R | 15 | ||||
| -rw-r--r-- | log/test.log | 18 | ||||
| -rw-r--r-- | tests/testthat/test_saemix_parent.R | 4 |
4 files changed, 26 insertions, 13 deletions
@@ -1,6 +1,6 @@ # mkin 1.1.2 -- 'R/saem.R': Implement and test saemix transformations for HS. +- 'R/saem.R': Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported. - 'R/convergence.R': New generic to show convergence information with a method for 'mmin' objects. @@ -253,6 +253,7 @@ saemix_model <- function(object, solution_type = "auto", transformations = c("mk degparms_fixed <- object[[1]]$bparms.fixed # Transformations are done in the degradation function by default + # (transformations = "mkin") transform.par = rep(0, length(degparms_optim)) odeini_optim_parm_names <- grep('_0$', names(degparms_optim), value = TRUE) @@ -276,6 +277,9 @@ saemix_model <- function(object, solution_type = "auto", transformations = c("mk if (length(mkin_model$spec) == 1) { parent_type <- mkin_model$spec[[1]]$type if (length(odeini_fixed) == 1) { + if (transformations == "saemix") { + stop("saemix transformations are not supported for parent fits with fixed initial parent value") + } if (parent_type == "SFO") { stop("saemix needs at least two parameters to work on.") } @@ -316,8 +320,15 @@ saemix_model <- function(object, solution_type = "auto", transformations = c("mk } } if (parent_type == "FOMC") { - model_function <- function(psi, id, xidep) { - psi[id, 1] / (xidep[, "time"]/exp(psi[id, 3]) + 1)^exp(psi[id, 2]) + if (transformations == "mkin") { + model_function <- function(psi, id, xidep) { + psi[id, 1] / (xidep[, "time"]/exp(psi[id, 3]) + 1)^exp(psi[id, 2]) + } + } else { + model_function <- function(psi, id, xidep) { + psi[id, 1] / (xidep[, "time"]/psi[id, 3] + 1)^psi[id, 2] + } + transform.par = c(0, 1, 1) } } if (parent_type == "DFOP") { diff --git a/log/test.log b/log/test.log index 776b6f49..67ba8841 100644 --- a/log/test.log +++ b/log/test.log @@ -5,12 +5,12 @@ ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.0s] -✔ | 1 12 | Dimethenamid data from 2018 [32.0s] +✔ | 1 12 | Dimethenamid data from 2018 [32.9s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_dmta.R:98:3): 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 [5.1s] +✔ | 14 | Error model fitting [5.0s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s] @@ -27,23 +27,23 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.4s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.8s] -✔ | 9 | Nonlinear mixed-effects models with nlme [9.1s] -✔ | 16 | Plotting [10.7s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.3s] +✔ | 16 | Plotting [10.6s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 27 | saemix parent models [178.6s] +✔ | 28 | saemix parent models [182.2s] ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] -✔ | 7 | Fitting the SFORB model [3.6s] +✔ | 7 | Fitting the SFORB model [3.9s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s] -✔ | 9 | Hypothesis tests [7.8s] +✔ | 9 | Hypothesis tests [7.7s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 263.0 s +Duration: 266.8 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 227 ] +[ FAIL 0 | WARN 0 | SKIP 2 | PASS 228 ] diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R index 7f550999..5d9a01de 100644 --- a/tests/testthat/test_saemix_parent.R +++ b/tests/testthat/test_saemix_parent.R @@ -30,12 +30,14 @@ test_that("Parent fits using saemix are correctly implemented", { round(s_sfo_n$confint_back["k_parent", "est."], 3)) mmkin_fomc_1 <- mmkin("FOMC", ds_fomc, quiet = TRUE, error_model = "tc", cores = n_cores) - fomc_saem_1 <- saem(mmkin_fomc_1, quiet = TRUE) + fomc_saem_1 <- saem(mmkin_fomc_1, quiet = TRUE, transformations = "saemix") + fomc_saem_2 <- saem(mmkin_fomc_1, quiet = TRUE, transformations = "mkin") ci_fomc_s1 <- summary(fomc_saem_1)$confint_back fomc_pop <- as.numeric(fomc_pop) expect_true(all(ci_fomc_s1[, "lower"] < fomc_pop)) expect_true(all(ci_fomc_s1[, "upper"] > fomc_pop)) + expect_equal(endpoints(fomc_saem_1), endpoints(fomc_saem_2), tol = 0.01) mmkin_fomc_2 <- update(mmkin_fomc_1, state.ini = 100, fixed_initials = "parent") fomc_saem_2 <- saem(mmkin_fomc_2, quiet = TRUE, transformations = "mkin") |