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(-) 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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