diff options
| -rw-r--r-- | NAMESPACE | 1 | ||||
| -rw-r--r-- | R/mhmkin.R | 39 | ||||
| -rw-r--r-- | R/status.R | 43 | ||||
| -rw-r--r-- | log/test.log | 40 | ||||
| -rw-r--r-- | man/status.Rd | 6 |
5 files changed, 70 insertions, 59 deletions
@@ -61,6 +61,7 @@ S3method(print,summary.nlme.mmkin) S3method(print,summary.saem.mmkin) S3method(residuals,mkinfit) S3method(saem,mmkin) +S3method(status,mhmkin) S3method(status,mmkin) S3method(status,multistart) S3method(status,multistart.saem.mmkin) @@ -136,45 +136,6 @@ print.mhmkin <- function(x, ...) { print(status(x)) } -status.mhmkin <- function(object, ...) { - if (inherits(object[[1]], "saem.mmkin")) { - test_func <- function(fit) { - if (inherits(fit$so, "try-error")) { - return("E") - } else { - if (!is.null(fit$FIM_failed)) { - return_values <- c("fixed effects" = "Fth", - "random effects and error model parameters" = "FO") - return(paste(return_values[fit$FIM_failed], collapse = ", ")) - } else { - return("OK") - } - } - } - } else { - stop("Only mhmkin objects containing saem.mmkin objects currently supported") - } - result <- lapply(object, test_func) - result <- unlist(result) - dim(result) <- dim(object) - dimnames(result) <- dimnames(object) - - class(result) <- "status.mhmkin" - return(result) -} - -#' @export -print.status.mhmkin <- function(x, ...) { - class(x) <- NULL - print(x, quote = FALSE) - cat("\n") - if (any(x == "OK")) cat("OK: Fit terminated successfully\n") - if (any(x == "Fth")) cat("Fth: Could not invert FIM for fixed effects\n") - if (any(x == "FO")) cat("FO: Could not invert FIM for random effects and error model parameters\n") - if (any(x == "Fth, FO")) cat("Fth, FO: Could not invert FIM for fixed effects, nor for random effects and error model parameters\n") - if (any(x == "E")) cat("E: Error\n") -} - #' @export AIC.mhmkin <- function(object, ..., k = 2) { if (inherits(object[[1]], "saem.mmkin")) { @@ -68,3 +68,46 @@ print.status.mmkin <- function(x, ...) { if (any(x == "OK")) cat("OK: No warnings\n") if (any(x == "E")) cat("E: Error\n") } + +#' @rdname status +#' @export +status.mhmkin <- function(object, ...) { + if (inherits(object[[1]], "saem.mmkin")) { + test_func <- function(fit) { + if (inherits(fit$so, "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 = ", ")) + } else { + return("OK") + } + } + } + } else { + stop("Only mhmkin objects containing saem.mmkin objects currently supported") + } + result <- lapply(object, test_func) + result <- unlist(result) + dim(result) <- dim(object) + dimnames(result) <- dimnames(object) + + class(result) <- "status.mhmkin" + return(result) +} + +#' @rdname status +#' @export +print.status.mhmkin <- function(x, ...) { + class(x) <- NULL + print(x, quote = FALSE) + cat("\n") + if (any(x == "OK")) cat("OK: Fit terminated successfully\n") + if (any(x == "Fth")) cat("Fth: Could not invert FIM for fixed effects\n") + if (any(x == "FO")) cat("FO: Could not invert FIM for random effects and error model parameters\n") + if (any(x == "Fth, FO")) cat("Fth, FO: Could not invert FIM for fixed effects, nor for random effects and error model parameters\n") + if (any(x == "E")) cat("E: Error\n") +} + diff --git a/log/test.log b/log/test.log index dee62073..429a2e02 100644 --- a/log/test.log +++ b/log/test.log @@ -1,53 +1,53 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.4s] +✔ | 5 | Analytical solutions for coupled models [3.3s] ✔ | 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 [32.5s] +✔ | 1 12 | Dimethenamid data from 2018 [43.2s] ──────────────────────────────────────────────────────────────────────────────── 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 [5.0s] +✔ | 14 | Error model fitting [11.5s] ✔ | 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 [0.4s] -✔ | 1 | Fitting the logistic model [0.2s] -✔ | 7 | Batch fitting and diagnosing hierarchical kinetic models [14.5s] -✔ | 1 12 | Nonlinear mixed-effects models [0.3s] +✔ | 4 | Calculation of FOCUS chi2 error levels [1.3s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.9s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.9s] +✔ | 1 | Fitting the logistic model [0.6s] +✔ | 7 | Batch fitting and diagnosing hierarchical kinetic models [30.9s] +✔ | 1 12 | Nonlinear mixed-effects models [0.4s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_mixed.R:74:3): 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 [0.4s] -✔ | 3 | mkinfit features [0.7s] -✔ | 8 | mkinmod model generation and printing [0.2s] +✔ | 10 | Special cases of mkinfit calls [0.7s] +✔ | 3 | mkinfit features [1.0s] +✔ | 8 | mkinmod model generation and printing [0.3s] ✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 7 | Multistart method for saem.mmkin models [37.6s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.7s] +✔ | 7 | Multistart method for saem.mmkin models [39.8s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.6s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.8s] ✔ | 16 | Plotting [10.1s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [72.8s] +✔ | 1 36 | saemix parent models [72.3s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_saemix_parent.R:152:3): 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] ✔ | 11 | Processing of residue series -✔ | 7 | Fitting the SFORB model [3.7s] +✔ | 7 | Fitting the SFORB model [3.8s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] -✔ | 9 | Hypothesis tests [8.3s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.1s] +✔ | 9 | Hypothesis tests [8.0s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 210.4 s +Duration: 249.3 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) diff --git a/man/status.Rd b/man/status.Rd index 8ff3531b..1cadbfcc 100644 --- a/man/status.Rd +++ b/man/status.Rd @@ -4,6 +4,8 @@ \alias{status} \alias{status.mmkin} \alias{print.status.mmkin} +\alias{status.mhmkin} +\alias{print.status.mhmkin} \title{Method to get status information for fit array objects} \usage{ status(object, ...) @@ -11,6 +13,10 @@ status(object, ...) \method{status}{mmkin}(object, ...) \method{print}{status.mmkin}(x, ...) + +\method{status}{mhmkin}(object, ...) + +\method{print}{status.mhmkin}(x, ...) } \arguments{ \item{object}{The object to investigate} |