From fe411af3dbed474d9e5b3cc1d509f66bd76f7319 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 28 Nov 2025 09:20:07 +0100 Subject: Example evaluation of D24_2014, improve docs --- DESCRIPTION | 2 +- R/D24_2014.R | 10 ++++ R/mkinds.R | 7 ++- R/saem.R | 8 ++- docs/404.html | 2 +- docs/articles/index.html | 2 +- docs/articles/web_only/mesotrione_parent_2023.html | 65 ++++++++++----------- docs/authors.html | 6 +- docs/index.html | 2 +- docs/news/index.html | 2 +- docs/reference/D24_2014-1.png | Bin 0 -> 88185 bytes docs/reference/D24_2014.html | 27 ++++++++- docs/reference/index.html | 2 +- docs/reference/mkinds.html | 12 ++-- docs/reference/mkindsg.html | 12 +++- docs/reference/saem.html | 39 ++++--------- docs/search.json | 2 +- man/D24_2014.Rd | 10 ++++ man/mkinds.Rd | 2 +- man/mkindsg.Rd | 5 ++ man/saem.Rd | 8 ++- 21 files changed, 134 insertions(+), 91 deletions(-) create mode 100644 docs/reference/D24_2014-1.png diff --git a/DESCRIPTION b/DESCRIPTION index a27dfe78..77b53a6d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -35,4 +35,4 @@ VignetteBuilder: knitr BugReports: https://github.com/jranke/mkin/issues/ URL: https://pkgdown.jrwb.de/mkin/ Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.2.9000 +RoxygenNote: 7.3.3 diff --git a/R/D24_2014.R b/R/D24_2014.R index aaed029c..973cf47d 100644 --- a/R/D24_2014.R +++ b/R/D24_2014.R @@ -33,5 +33,15 @@ #' DCP = mkinsub("SFO", to = "DCA"), #' DCA = mkinsub("SFO")) #' print(m_D24_2) +#' D24_2014_data <- lapply(D24_2014$ds, function(x) x$data) +#' names(D24_2014_data) <- sapply(D24_2014$ds, function(x) x$title) +#' f_D24_2014 <- mmkin( +#' models = list( +#' "SFO-SFO-SFO" = m_D24, +#' "DFOP-SFO-SFO" = m_D24_2), +#' data = D24_2014_data, +#' quiet = TRUE) +#' print(f_D24_2014) +#' plot(f_D24_2014[, 3]) #' } "D24_2014" diff --git a/R/mkinds.R b/R/mkinds.R index df66ab0f..e6c153b8 100644 --- a/R/mkinds.R +++ b/R/mkinds.R @@ -3,7 +3,7 @@ #' @description #' At the moment this dataset class is hardly used in mkin. For example, #' mkinfit does not take mkinds datasets as argument, but works with dataframes -#' such as the on contained in the data field of mkinds objects. Some datasets +#' such as the one contained in the data field of mkinds objects. Some datasets #' provided by this package come as mkinds objects nevertheless. #' #' @importFrom R6 R6Class @@ -87,6 +87,11 @@ print.mkinds <- function(x, data = FALSE, ...) { #' Time normalisation factors are initialised with a value of 1 for each #' dataset if no data are supplied. #' +#' @note +#' Currently, no functions making use of the defined class structure +#' are available in this package. Refer to [D24_2014] for an example +#' dataset in this structure, with some example evaluations. +#' #' @examples #' #' mdsg <- mkindsg$new("Experimental X", experimental_data_for_UBA_2019[6:10]) diff --git a/R/saem.R b/R/saem.R index 2a9c2fa5..79c8a518 100644 --- a/R/saem.R +++ b/R/saem.R @@ -122,9 +122,11 @@ utils::globalVariables(c("predicted", "std")) #' plot(f_saem_dfop_sfo) #' summary(f_saem_dfop_sfo, data = TRUE) #' -#' # The following takes about 6 minutes -#' f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve", -#' nbiter.saemix = c(200, 80)) +#' # The following took about 6 minutes and currently fails with +#' # "Error in deSolve::lsoda(y = odeini, times = outtimes_deSolve, func = lsoda_func, : +#' # illegal input detected before taking any integration steps - see written message" +#' #f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve", +#' # nbiter.saemix = c(200, 80)) #' #' #anova( #' # f_saem_dfop_sfo, diff --git a/docs/404.html b/docs/404.html index 4a18a694..ce758d30 100644 --- a/docs/404.html +++ b/docs/404.html @@ -20,7 +20,7 @@ mkin - 1.2.11 + 1.2.10