diff options
| -rw-r--r-- | DESCRIPTION | 4 | ||||
| -rw-r--r-- | NEWS.md | 4 | ||||
| -rw-r--r-- | R/mhmkin.R | 28 | ||||
| -rw-r--r-- | R/status.R | 18 | ||||
| -rw-r--r-- | log/build.log | 2 | ||||
| -rw-r--r-- | log/check.log | 6 | ||||
| -rw-r--r-- | log/test.log | 24 | ||||
| -rw-r--r-- | man/check_failed.Rd | 14 |
8 files changed, 68 insertions, 32 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index ae0fdc2c..0d924faf 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 1.2.7 -Date: 2023-11-25 +Version: 1.2.8 +Date: 2023-11-26 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "johannes.ranke@jrwb.de", @@ -1,3 +1,7 @@ +# mkin 1.2.8 + +- 'R/{mhmkin,status}.R': Deal with 'saem' fits that fail when updating an 'mhmkin' object + # mkin 1.2.7 - 'R/illparms.R': Fix a bug that prevented an ill-defined random effect to be found if there was only one random effect in the model. Also add a test for this. @@ -219,11 +219,22 @@ print.mhmkin <- function(x, ...) { print(status(x)) } +#' Check if fit within an mhmkin object failed +#' @param x The object to be checked +check_failed <- function(x) { + if (inherits(x, "try-error")) { + return(TRUE) + } else { + if (inherits(x$so, "try-error")) { + return(TRUE) + } else { + return(FALSE) + } + } +} + #' @export AIC.mhmkin <- function(object, ..., k = 2) { - if (inherits(object[[1]], "saem.mmkin")) { - check_failed <- function(x) if (inherits(x$so, "try-error")) TRUE else FALSE - } res <- sapply(object, function(x) { if (check_failed(x)) return(NA) else return(AIC(x$so, k = k)) @@ -235,9 +246,6 @@ AIC.mhmkin <- function(object, ..., k = 2) { #' @export BIC.mhmkin <- function(object, ...) { - if (inherits(object[[1]], "saem.mmkin")) { - check_failed <- function(x) if (inherits(x$so, "try-error")) TRUE else FALSE - } res <- sapply(object, function(x) { if (check_failed(x)) return(NA) else return(BIC(x$so)) @@ -280,7 +288,13 @@ anova.mhmkin <- function(object, ..., if (identical(model.names, "auto")) { model.names <- outer(rownames(object), colnames(object), paste) } - rlang::inject(anova(!!!(object), method = method, test = test, + failed_index <- which(sapply(object, check_failed), arr.ind = TRUE) + if (length(failed_index > 0)) { + rlang::inject(anova(!!!(object[-failed_index]), method = method, test = test, + model.names = model.names[-failed_index])) + } else { + rlang::inject(anova(!!!(object), method = method, test = test, model.names = model.names)) + } } @@ -74,15 +74,19 @@ print.status.mmkin <- function(x, ...) { status.mhmkin <- function(object, ...) { if (inherits(object[[1]], "saem.mmkin")) { test_func <- function(fit) { - if (inherits(fit$so, "try-error")) { - return("E") + if (inherits(fit, "try-error")) { + return("E") } else { - if (!is.null(fit$FIM_failed)) { - return_values <- c("fixed effects" = "Fth", - "random effects and error model parameters" = "FO") - return(paste(return_values[fit$FIM_failed], collapse = ", ")) + if (inherits(fit$so, "try-error")) { + return("E") } else { - return("OK") + if (!is.null(fit$FIM_failed)) { + return_values <- c("fixed effects" = "Fth", + "random effects and error model parameters" = "FO") + return(paste(return_values[fit$FIM_failed], collapse = ", ")) + } else { + return("OK") + } } } } diff --git a/log/build.log b/log/build.log index b4269860..c2001830 100644 --- a/log/build.log +++ b/log/build.log @@ -7,5 +7,5 @@ * checking for empty or unneeded directories Removed empty directory ‘mkin/inst/rmarkdown/templates/hierarchical_kinetics_parent’ Removed empty directory ‘mkin/vignettes/web_only’ -* building ‘mkin_1.2.7.tar.gz’ +* building ‘mkin_1.2.8.tar.gz’ diff --git a/log/check.log b/log/check.log index 26fdc5a0..5e777a87 100644 --- a/log/check.log +++ b/log/check.log @@ -9,9 +9,9 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.2.7’ +* this is package ‘mkin’ version ‘1.2.8’ * package encoding: UTF-8 -* checking CRAN incoming feasibility ... [2s/15s] Note_to_CRAN_maintainers +* checking CRAN incoming feasibility ... [2s/14s] Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ * checking package namespace information ... OK * checking package dependencies ... OK @@ -62,7 +62,7 @@ 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 ... [10s/10s] OK +* checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK diff --git a/log/test.log b/log/test.log index a6ac83ed..9dc63675 100644 --- a/log/test.log +++ b/log/test.log @@ -4,39 +4,39 @@ ✔ | 5 | Analytical solutions for coupled models [1.5s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 6 | Use of precompiled symbols in mkinpredict [3.3s] +✔ | 6 | Use of precompiled symbols in mkinpredict [3.2s] ✔ | 12 | Confidence intervals and p-values -✔ | 1 12 | Dimethenamid data from 2018 [13.1s] +✔ | 1 12 | Dimethenamid data from 2018 [13.8s] ✔ | 14 | Error model fitting [2.5s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 4 | Test fitting the decline of metabolites from their maximum ✔ | 1 | Fitting the logistic model -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [20.4s] -✔ | 2 16 | Nonlinear mixed-effects models [149.9s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.8s] +✔ | 2 16 | Nonlinear mixed-effects models [149.6s] ✔ | 3 | Test dataset classes mkinds and mkindsg ✔ | 10 | Special cases of mkinfit calls ✔ | 3 | mkinfit features ✔ | 8 | mkinmod model generation and printing ✔ | 3 | Model predictions with mkinpredict -✔ | 12 | Multistart method for saem.mmkin models [23.0s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] -✔ | 9 | Nonlinear mixed-effects models with nlme [3.6s] -✔ | 15 | Plotting [4.8s] +✔ | 12 | Multistart method for saem.mmkin models [23.6s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6s] +✔ | 9 | Nonlinear mixed-effects models with nlme [4.0s] +✔ | 15 | Plotting [4.7s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 38 | saemix parent models [35.2s] +✔ | 1 38 | saemix parent models [36.4s] ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [1.6s] +✔ | 10 | Fitting the SFORB model [1.8s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) -✔ | 9 | Hypothesis tests [2.8s] +✔ | 9 | Hypothesis tests [3.1s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 268.2 s +Duration: 270.7 s ── Skipped tests (4) ─────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 5 minutes on my new system diff --git a/man/check_failed.Rd b/man/check_failed.Rd new file mode 100644 index 00000000..85029024 --- /dev/null +++ b/man/check_failed.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/mhmkin.R +\name{check_failed} +\alias{check_failed} +\title{Check if fit within an mhmkin object failed} +\usage{ +check_failed(x) +} +\arguments{ +\item{x}{The object to be checked} +} +\description{ +Check if fit within an mhmkin object failed +} |