From 43af185533b11327368148a44e9295ea3eb3abb1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 23 Nov 2023 06:17:28 +0100 Subject: Bump version, fix test from last commit, check and test --- man/hierarchical_kinetics.Rd | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) (limited to 'man') diff --git a/man/hierarchical_kinetics.Rd b/man/hierarchical_kinetics.Rd index bcbe1e06..8330fe68 100644 --- a/man/hierarchical_kinetics.Rd +++ b/man/hierarchical_kinetics.Rd @@ -9,7 +9,11 @@ hierarchical_kinetics(..., keep_tex = FALSE) \arguments{ \item{...}{Arguments to \code{rmarkdown::pdf_document}} -\item{keep_tex}{Keep the intermediate tex file used in the conversion to PDF} +\item{keep_tex}{Keep the intermediate tex file used in the conversion to PDF. +Note that this argument does not control whether to keep the auxiliary +files (e.g., \file{.aux}) generated by LaTeX when compiling \file{.tex} to +\file{.pdf}. To keep these files, you may set \code{options(tinytex.clean = +FALSE)}.} } \value{ R Markdown output format to pass to -- cgit v1.2.3 From b07f9fcb7468ac1b5fab0924328fba36ae943be5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 26 Nov 2023 20:38:30 +0100 Subject: Deal with 'saem' fits failing when updating an 'mhmkin' object --- DESCRIPTION | 4 ++-- NEWS.md | 4 ++++ R/mhmkin.R | 28 +++++++++++++++++++++------- R/status.R | 18 +++++++++++------- log/build.log | 2 +- log/check.log | 6 +++--- log/test.log | 24 ++++++++++++------------ man/check_failed.Rd | 14 ++++++++++++++ 8 files changed, 68 insertions(+), 32 deletions(-) create mode 100644 man/check_failed.Rd (limited to 'man') 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", diff --git a/NEWS.md b/NEWS.md index 100f8b6c..f7c38915 100644 --- a/NEWS.md +++ b/NEWS.md @@ -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. diff --git a/R/mhmkin.R b/R/mhmkin.R index 6265a59e..14a7ac29 100644 --- a/R/mhmkin.R +++ b/R/mhmkin.R @@ -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$so)) @@ -280,7 +288,13 @@ anova.mhmkin <- function(object, ..., if (identical(model.names, "auto")) { model.names <- outer(rownames(object), colnames(object), paste) } - rlang::inject(anova(!!!(object), method = method, test = test, + failed_index <- which(sapply(object, check_failed), arr.ind = TRUE) + if (length(failed_index > 0)) { + rlang::inject(anova(!!!(object[-failed_index]), method = method, test = test, + model.names = model.names[-failed_index])) + } else { + rlang::inject(anova(!!!(object), method = method, test = test, model.names = model.names)) + } } diff --git a/R/status.R b/R/status.R index 8bcd3a16..f9d79e7d 100644 --- a/R/status.R +++ b/R/status.R @@ -74,15 +74,19 @@ print.status.mmkin <- function(x, ...) { status.mhmkin <- function(object, ...) { if (inherits(object[[1]], "saem.mmkin")) { test_func <- function(fit) { - if (inherits(fit$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 ’ * checking package namespace information ... OK * checking package dependencies ... OK @@ -62,7 +62,7 @@ Maintainer: ‘Johannes Ranke ’ * 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 +} -- cgit v1.2.3 From e5aea600fd957955fc3e8e41dbc93bf4f65af803 Mon Sep 17 00:00:00 2001 From: Ranke Johannes Date: Thu, 19 Dec 2024 10:59:44 +0100 Subject: Support observed data as tibble Closes #14 --- DESCRIPTION | 2 +- NEWS.md | 2 + R/mkinfit.R | 6 +- log/build.log | 3 +- man/mkinfit.Rd | 3 +- man/mkinpredict.Rd | 4 +- vignettes/FOCUS_D.html | 126 +++++++------- vignettes/FOCUS_L.html | 435 +++++++++++++++++++++++++------------------------ vignettes/mkin.html | 213 ++++++++++++------------ 9 files changed, 402 insertions(+), 392 deletions(-) (limited to 'man') diff --git a/DESCRIPTION b/DESCRIPTION index 50c6cec3..2af8a0ed 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -36,4 +36,4 @@ VignetteBuilder: knitr BugReports: https://github.com/jranke/mkin/issues/ URL: https://pkgdown.jrwb.de/mkin/ Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.2.9000 diff --git a/NEWS.md b/NEWS.md index 2ac1f037..f307f71d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # mkin 1.2.9 +- 'R/mkinfit.R': Support passing the observed data as a 'tibble' + - 'R/parplot.R': Support multistart objects with covariate models and filter negative values of scaled parameters (with a warning) for plotting. - 'R/create_deg_func.R: Make sure that no reversible reactions are specified in the case of two observed variables, as this is not supported diff --git a/R/mkinfit.R b/R/mkinfit.R index c851fddb..52053685 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -21,7 +21,8 @@ utils::globalVariables(c("name", "time", "value")) #' "FOMC", "DFOP", "HS", "SFORB", "IORE"). If a shorthand name is given, a #' parent only degradation model is generated for the variable with the #' highest value in \code{observed}. -#' @param observed A dataframe with the observed data. The first column called +#' @param observed A dataframe or an object coercible to a dataframe +#' (e.g. a \code{tibble}) with the observed data. The first column called #' "name" must contain the name of the observed variable for each data point. #' The second column must contain the times of observation, named "time". #' The third column must be named "value" and contain the observed values. @@ -292,6 +293,9 @@ mkinfit <- function(mkinmod, observed, # Get the names of observed variables obs_vars <- names(mkinmod$spec) + # Coerce observed data to a dataframe + observed <- as.data.frame(observed) + # Subset observed data with names of observed data in the model and remove NA values observed <- subset(observed, name %in% obs_vars) observed <- subset(observed, !is.na(value)) diff --git a/log/build.log b/log/build.log index de7e4488..ce7cc8e1 100644 --- a/log/build.log +++ b/log/build.log @@ -5,7 +5,8 @@ * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * 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_1.2.9.tar.gz’ +Warning: invalid uid value replaced by that for user 'nobody' +Warning: invalid gid value replaced by that for user 'nobody' diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index f96b4d22..edec9546 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -39,7 +39,8 @@ model to be fitted to the data, or one of the shorthand names ("SFO", parent only degradation model is generated for the variable with the highest value in \code{observed}.} -\item{observed}{A dataframe with the observed data. The first column called +\item{observed}{A dataframe or an object coercible to a dataframe +(e.g. a \code{tibble}) with the observed data. The first column called "name" must contain the name of the observed variable for each data point. The second column must contain the times of observation, named "time". The third column must be named "value" and contain the observed values. diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd index 792d0e47..4db4d62f 100644 --- a/man/mkinpredict.Rd +++ b/man/mkinpredict.Rd @@ -71,7 +71,7 @@ parent compound.} \item{use_symbols}{If set to \code{TRUE} (default), symbol info present in the \link{mkinmod} object is used if available for accessing compiled code} -\item{method.ode}{The solution method passed via \link{mkinpredict} to \link{ode}] in +\item{method.ode}{The solution method passed via \link{mkinpredict} to \link[deSolve:ode]{deSolve::ode}] in case the solution type is "deSolve" and we are not using compiled code. When using compiled code, only lsoda is supported.} @@ -86,7 +86,7 @@ the observed variables (default) or for all state variables (if set to FALSE). Setting this to FALSE has no effect for analytical solutions, as these always return mapped output.} -\item{na_stop}{Should it be an error if \link{ode} returns NaN values} +\item{na_stop}{Should it be an error if \link[deSolve:ode]{deSolve::ode} returns NaN values} } \value{ A matrix with the numeric solution in wide format diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index d27b4767..9cf020ec 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -31,7 +31,7 @@ document.addEventListener('DOMContentLoaded', function(e) { !function(e,t){"use strict";"object"==typeof module&&"object"==typeof module.exports?module.exports=e.document?t(e,!0):function(e){if(!e.document)throw new Error("jQuery requires a window with a document");return t(e)}:t(e)}("undefined"!=typeof window?window:this,function(C,e){"use strict";var t=[],r=Object.getPrototypeOf,s=t.slice,g=t.flat?function(e){return t.flat.call(e)}:function(e){return 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-

Site built with pkgdown 2.1.0.

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Site built with pkgdown 2.1.1.

diff --git a/docs/news/index.html b/docs/news/index.html index eeb84a76..44de0536 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -656,7 +656,7 @@
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Site built with pkgdown 2.1.0.

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diff --git a/docs/reference/index.html b/docs/reference/index.html index 63e1e634..1448bbe6 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -722,7 +722,7 @@
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diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 860c7cfc..13f42da0 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -1,78 +1,65 @@ -Produce predictions from a kinetic model using specific parameters — mkinpredict • mkinProduce predictions from a kinetic model using specific parameters — mkinpredict • mkin +kinetic parameters and initial values for the state variables."> Skip to contents - -