diff options
| -rw-r--r-- | NEWS.md | 4 | ||||
| -rw-r--r-- | R/summary.saem.mmkin.R | 11 | ||||
| -rw-r--r-- | log/check.log | 11 | ||||
| -rw-r--r-- | log/test.log | 26 | ||||
| -rw-r--r-- | man/summary.saem.mmkin.Rd | 17 |
5 files changed, 49 insertions, 20 deletions
@@ -1,10 +1,10 @@ # mkin 1.2.3 -- Depend on upcoming deSolve version with the possibility to avoid resolving symbols in a shared library (compiled models) over and over. +- Depend on current deSolve version with the possibility to avoid resolving symbols in a shared library (compiled models) over and over, thanks to Thomas Petzoldt. - 'R/mkinerrmin.R': Fix typo in subset (use of = instead of ==), thanks to Sebastian Meyer for spotting this during his work on R 4.3.0. -- 'R/{endpoints,parms,plot.mixed.mmkin}.R': Calculate parameters and endpoints and plot population curves for specific covariate values, or specific percentiles of covariate values used in saem fits. +- 'R/{endpoints,parms,plot.mixed.mmkin,summary.saem.mmkin}.R': Calculate parameters and endpoints and plot population curves for specific covariate values, or specific percentiles of covariate values used in saem fits. # mkin 1.2.2 (unreleased) diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R index 49b02a50..c470ccf0 100644 --- a/R/summary.saem.mmkin.R +++ b/R/summary.saem.mmkin.R @@ -15,6 +15,7 @@ #' included. #' @param digits Number of digits to use for printing #' @param \dots optional arguments passed to methods like \code{print}. +#' @inheritParams endpoints #' @return The summary function returns a list based on the [saemix::SaemixObject] #' obtained in the fit, with at least the following additional components #' \item{saemixversion, mkinversion, Rversion}{The saemix, mkin and R versions used} @@ -93,7 +94,9 @@ #' } #' #' @export -summary.saem.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes = TRUE, ...) { +summary.saem.mmkin <- function(object, data = FALSE, verbose = FALSE, + covariates = NULL, covariate_quantile = 0.5, + distimes = TRUE, ...) { mod_vars <- names(object$mkinmod$diffs) @@ -199,6 +202,7 @@ summary.saem.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes = } ep <- endpoints(object) + object$covariates <- ep$covariates if (length(ep$ff) != 0) object$ff <- ep$ff if (distimes) object$distimes <- ep$distimes @@ -281,6 +285,11 @@ print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3) print(x$confint_back, digits = digits) } + if (!is.null(x$covariates)) { + cat("\nCovariates used for endpoints below:\n") + print(x$covariates) + } + printSFORB <- !is.null(x$SFORB) if(printSFORB){ cat("\nEstimated Eigenvalues of SFORB model(s):\n") diff --git a/log/check.log b/log/check.log index 9f05935f..cb313bc0 100644 --- a/log/check.log +++ b/log/check.log @@ -21,7 +21,8 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ * checking whether package ‘mkin’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK -* checking for future file timestamps ... OK +* checking for future file timestamps ... NOTE +unable to verify current time * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK @@ -58,7 +59,7 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [11s/11s] OK +* checking examples ... [10s/11s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK @@ -70,5 +71,9 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ * checking for detritus in the temp directory ... OK * DONE -Status: OK +Status: 1 NOTE +See + ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ +for details. + diff --git a/log/test.log b/log/test.log index de28f836..54aa3c73 100644 --- a/log/test.log +++ b/log/test.log @@ -4,50 +4,50 @@ ✔ | 5 | Analytical solutions for coupled models [1.6s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 12 | Confidence intervals and p-values [0.4s] -✔ | 1 12 | Dimethenamid data from 2018 [12.0s] +✔ | 12 | Confidence intervals and p-values [0.3s] +✔ | 1 12 | Dimethenamid data from 2018 [12.5s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_dmta.R:99'): 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 [2.3s] +✔ | 14 | Error model fitting [2.4s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.3s] -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.4s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.5s] ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.2s] ✔ | 1 | Fitting the logistic model [0.1s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.0s] -✔ | 1 11 | Nonlinear mixed-effects models [5.9s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.5s] +✔ | 1 11 | Nonlinear mixed-effects models [5.7s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_mixed.R:78'): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve ──────────────────────────────────────────────────────────────────────────────── ✔ | 3 | Test dataset classes mkinds and mkindsg -✔ | 10 | Special cases of mkinfit calls [0.5s] +✔ | 10 | Special cases of mkinfit calls [0.4s] ✔ | 3 | mkinfit features [0.5s] ✔ | 8 | mkinmod model generation and printing ✔ | 3 | Model predictions with mkinpredict [0.1s] -✔ | 12 | Multistart method for saem.mmkin models [21.7s] +✔ | 12 | Multistart method for saem.mmkin models [21.2s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] ✔ | 9 | Nonlinear mixed-effects models with nlme [3.7s] -✔ | 15 | Plotting [4.9s] +✔ | 15 | Plotting [4.4s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [32.6s] +✔ | 1 36 | saemix parent models [30.8s] ──────────────────────────────────────────────────────────────────────────────── 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 [0.5s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [1.7s] +✔ | 10 | Fitting the SFORB model [1.6s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.8s] -✔ | 9 | Hypothesis tests [3.0s] +✔ | 9 | Hypothesis tests [2.9s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 114.8 s +Duration: 112.6 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) diff --git a/man/summary.saem.mmkin.Rd b/man/summary.saem.mmkin.Rd index 0845d4d2..41932547 100644 --- a/man/summary.saem.mmkin.Rd +++ b/man/summary.saem.mmkin.Rd @@ -5,7 +5,15 @@ \alias{print.summary.saem.mmkin} \title{Summary method for class "saem.mmkin"} \usage{ -\method{summary}{saem.mmkin}(object, data = FALSE, verbose = FALSE, distimes = TRUE, ...) +\method{summary}{saem.mmkin}( + object, + data = FALSE, + verbose = FALSE, + covariates = NULL, + covariate_quantile = 0.5, + distimes = TRUE, + ... +) \method{print}{summary.saem.mmkin}(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...) } @@ -17,6 +25,13 @@ the summary.} \item{verbose}{Should the summary be verbose?} +\item{covariates}{Numeric vector with covariate values for all variables in +any covariate models in the object. If given, it overrides 'covariate_quantile'.} + +\item{covariate_quantile}{This argument only has an effect if the fitted +object has covariate models. If so, the default is to show endpoints +for the median of the covariate values (50th percentile).} + \item{distimes}{logical, indicating whether DT50 and DT90 values should be included.} |