diff options
| -rw-r--r-- | NEWS.md | 2 | ||||
| -rw-r--r-- | R/illparms.R | 14 | ||||
| -rw-r--r-- | log/test.log | 41 | ||||
| -rw-r--r-- | man/illparms.Rd | 13 |
4 files changed, 43 insertions, 27 deletions
@@ -6,6 +6,8 @@ - 'R/parplot.R': Possibility to select the top 'llquant' fraction of the fits for the parameter plots, and improved legend text. +- 'R/illparms.R': Also check if confidence intervals for slope parameters in covariate models include zero. Only implemented for fits obtained with the saemix backend. + # mkin 1.2.1 (2022-11-19) - '{data,R}/ds_mixed.rda': Include the test data in the package instead of generating it in 'tests/testthat/setup_script.R'. Refactor the generating code to make it consistent and update tests. diff --git a/R/illparms.R b/R/illparms.R index 01e75cf1..eef4bd33 100644 --- a/R/illparms.R +++ b/R/illparms.R @@ -20,6 +20,9 @@ #' @param random For hierarchical fits, should random effects be tested? #' @param errmod For hierarchical fits, should error model parameters be #' tested? +#' @param slopes For hierarchical [saem] fits using saemix as backend, +#' should slope parameters in the covariate model(starting with 'beta_') be +#' tested? #' @return For [mkinfit] or [saem] objects, a character vector of parameter #' names. For [mmkin] or [mhmkin] objects, a matrix like object of class #' 'illparms.mmkin' or 'illparms.mhmkin'. @@ -92,7 +95,7 @@ print.illparms.mmkin <- function(x, ...) { #' @rdname illparms #' @export -illparms.saem.mmkin <- function(object, conf.level = 0.95, random = TRUE, errmod = TRUE, ...) { +illparms.saem.mmkin <- function(object, conf.level = 0.95, random = TRUE, errmod = TRUE, slopes = TRUE, ...) { if (inherits(object$so, "try-error")) { ill_parms <- NA } else { @@ -106,6 +109,15 @@ illparms.saem.mmkin <- function(object, conf.level = 0.95, random = TRUE, errmod ill_parms_errmod <- ints$errmod[, "lower"] < 0 & ints$errmod[, "est."] > 0 ill_parms <- c(ill_parms, names(which(ill_parms_errmod))) } + if (slopes) { + if (is.null(object$so)) stop("Slope testing is only implemented for the saemix backend") + slope_names <- grep("^beta_", object$so@model@name.fixed, value = TRUE) + ci <- object$so@results@conf.int + rownames(ci) <- ci$name + slope_ci <- ci[slope_names, ] + ill_parms_slopes <- slope_ci[, "lower"] < 0 & slope_ci[, "estimate"] > 0 + ill_parms <- c(ill_parms, slope_names[ill_parms_slopes]) + } } class(ill_parms) <- "illparms.saem.mmkin" return(ill_parms) diff --git a/log/test.log b/log/test.log index 7614b136..af2ffc41 100644 --- a/log/test.log +++ b/log/test.log @@ -1,23 +1,23 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.2s] +✔ | 5 | Analytical solutions for coupled models [3.4s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.1s] -✔ | 1 12 | Dimethenamid data from 2018 [32.0s] +✔ | 1 12 | Dimethenamid data from 2018 [32.7s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_dmta.R:98'): 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 [4.8s] +✔ | 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] -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s] ✔ | 1 | Fitting the logistic model [0.2s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [42.2s] -✔ | 1 11 | Nonlinear mixed-effects models [13.3s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [43.4s] +✔ | 1 11 | Nonlinear mixed-effects models [13.5s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_mixed.R:78'): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve @@ -27,40 +27,31 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve ✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.4s] -✖ | 1 11 | Multistart method for saem.mmkin models [46.7s] -──────────────────────────────────────────────────────────────────────────────── -Failure ('test_multistart.R:56'): multistart works for saem.mmkin models -Snapshot of `testcase` to 'multistart/parplot-for-dfop-sfo-fit.svg' has changed -Run `testthat::snapshot_review('multistart/')` to review changes -Backtrace: - 1. vdiffr::expect_doppelganger("parplot for dfop sfo fit", parplot_dfop_sfo) - at test_multistart.R:56:2 - 3. testthat::expect_snapshot_file(...) -──────────────────────────────────────────────────────────────────────────────── +✔ | 12 | Multistart method for saem.mmkin models [50.1s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.2s] -✔ | 9 | Nonlinear mixed-effects models with nlme [9.4s] -✔ | 15 | Plotting [10.1s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.8s] +✔ | 15 | Plotting [10.5s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [73.6s] +✔ | 1 36 | saemix parent models [85.7s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_saemix_parent.R:143'): We can also use mkin solution methods for saem Reason: This still takes almost 2.5 minutes although we do not solve ODEs ──────────────────────────────────────────────────────────────────────────────── -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.7s] +✔ | 10 | 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) [2.3s] -✔ | 9 | Hypothesis tests [8.1s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] +✔ | 9 | Hypothesis tests [8.2s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 260.9 s +Duration: 280.1 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) • This still takes almost 2.5 minutes although we do not solve ODEs (1) -[ FAIL 1 | WARN 0 | SKIP 3 | PASS 269 ] +[ FAIL 0 | WARN 0 | SKIP 3 | PASS 270 ] diff --git a/man/illparms.Rd b/man/illparms.Rd index 14be9c35..75eb18f0 100644 --- a/man/illparms.Rd +++ b/man/illparms.Rd @@ -22,7 +22,14 @@ illparms(object, ...) \method{print}{illparms.mmkin}(x, ...) -\method{illparms}{saem.mmkin}(object, conf.level = 0.95, random = TRUE, errmod = TRUE, ...) +\method{illparms}{saem.mmkin}( + object, + conf.level = 0.95, + random = TRUE, + errmod = TRUE, + slopes = TRUE, + ... +) \method{print}{illparms.saem.mmkin}(x, ...) @@ -43,6 +50,10 @@ illparms(object, ...) \item{errmod}{For hierarchical fits, should error model parameters be tested?} + +\item{slopes}{For hierarchical \link{saem} fits using saemix as backend, +should slope parameters in the covariate model(starting with 'beta_') be +tested?} } \value{ For \link{mkinfit} or \link{saem} objects, a character vector of parameter |