diff options
| -rw-r--r-- | R/mkinds.R | 53 | ||||
| -rw-r--r-- | docs/reference/mkinds.html | 64 | ||||
| -rw-r--r-- | docs/reference/print.mkinds.html | 6 | ||||
| -rw-r--r-- | man/mkinds.Rd | 55 | ||||
| -rw-r--r-- | man/print.mkinds.Rd | 2 | ||||
| -rw-r--r-- | test.log | 45 |
6 files changed, 126 insertions, 99 deletions
@@ -1,43 +1,50 @@ #' A dataset class for mkin #' -#' A dataset class for mkin -#' -#' @name mkinds -#' @docType class -#' @format An \code{\link{R6Class}} generator object. -#' @section Fields: -#' -#' \describe{ \item{list("title")}{A full title for the dataset} -#' -#' \item{list("sampling")}{times The sampling times} -#' -#' \item{list("time_unit")}{The time unit} -#' -#' \item{list("observed")}{Names of the observed compounds} -#' -#' \item{list("unit")}{The unit of the observations} -#' -#' \item{list("replicates")}{The number of replicates} -#' -#' \item{list("data")}{A dataframe with at least the columns name, time and -#' value in order to be compatible with mkinfit} } +#' @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 +#' provided by this package come as mkinds objects nevertheless. +#' #' @importFrom R6 R6Class -#' @keywords datasets +#' @seealso The S3 printing method \code{\link{print.mkinds}} #' @examples #' #' mds <- mkinds$new("FOCUS A", FOCUS_2006_A) +#' print(mds) #' #' @export mkinds <- R6Class("mkinds", public = list( + + #' @field title A full title for the dataset title = NULL, + + #' @field sampling_times The sampling times sampling_times = NULL, + + #' @field time_unit The time unit time_unit = NULL, + + #' @field observed Names of the observed variables observed = NULL, + + #' @field unit The unit of the observations unit = NULL, + + #' @field replicates The maximum number of replicates per sampling time replicates = NULL, + + #' @field data A data frame with at least the columns name, time + #' and value in order to be compatible with mkinfit data = NULL, + #' @description + #' Create a new mkinds object + #' @param title The dataset title + #' @param data The data + #' @param time_unit The time unit + #' @param unit The unit of the observations initialize = function(title = "", data, time_unit = NA, unit = NA) { self$title <- title @@ -56,8 +63,6 @@ mkinds <- R6Class("mkinds", #' Print mkinds objects #' -#' Print mkinds objects. -#' #' @param x An \code{\link{mkinds}} object. #' @param \dots Not used. #' @export diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index c1cdcf99..ef6fb35c 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -36,7 +36,10 @@ <meta property="og:title" content="A dataset class for mkin — mkinds" /> -<meta property="og:description" content="A dataset class for mkin" /> +<meta property="og:description" content="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 +provided by this package come as mkinds objects nevertheless." /> <meta name="twitter:card" content="summary" /> @@ -133,36 +136,36 @@ </div> <div class="ref-description"> - <p>A dataset class for mkin</p> + <p>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 +provided by this package come as mkinds objects nevertheless.</p> </div> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p>An <code>R6Class</code> generator object.</p> - <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2> + <div class='dont-index'><p>The S3 printing method <code><a href='print.mkinds.html'>print.mkinds</a></code></p></div> + <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2> - - - -<dl class='dl-horizontal'> -<dt>list("title")</dt><dd><p>A full title for the dataset</p></dd> + <p><div class="r6-fields"></p><dl class='dl-horizontal'> +<dt><code>title</code></dt><dd><p>A full title for the dataset</p></dd> -<dt>list("sampling")</dt><dd><p>times The sampling times</p></dd> +<dt><code>sampling_times</code></dt><dd><p>The sampling times</p></dd> -<dt>list("time_unit")</dt><dd><p>The time unit</p></dd> +<dt><code>time_unit</code></dt><dd><p>The time unit</p></dd> -<dt>list("observed")</dt><dd><p>Names of the observed compounds</p></dd> +<dt><code>observed</code></dt><dd><p>Names of the observed variables</p></dd> -<dt>list("unit")</dt><dd><p>The unit of the observations</p></dd> +<dt><code>unit</code></dt><dd><p>The unit of the observations</p></dd> -<dt>list("replicates")</dt><dd><p>The number of replicates</p></dd> +<dt><code>replicates</code></dt><dd><p>The maximum number of replicates per sampling time</p></dd> -<dt>list("data")</dt><dd><p>A dataframe with at least the columns name, time and -value in order to be compatible with mkinfit</p></dd> -</dl> +<dt><code>data</code></dt><dd><p>A data frame with at least the columns name, time +and value in order to be compatible with mkinfit</p></dd> +</dl><p></div></p> <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> @@ -174,10 +177,20 @@ value in order to be compatible with mkinfit</p></dd> </ul> <p><hr> <a id="method-new"></a></p><h3>Method <code>new()</code></h3> - -<h3>Usage</h3> +<p>Create a new mkinds object</p><h3>Usage</h3> <p><div class="r"></p><pre>mkinds$new(title = "", data, time_unit = NA, unit = NA)</pre><p></div></p> +<h3>Arguments</h3> +<p><div class="arguments"></p><dl class='dl-horizontal'> +<dt><code>title</code></dt><dd><p>The dataset title</p></dd> + +<dt><code>data</code></dt><dd><p>The data</p></dd> + +<dt><code>time_unit</code></dt><dd><p>The time unit</p></dd> + +<dt><code>unit</code></dt><dd><p>The unit of the observations</p></dd> + +</dl><p></div></p> <p><hr> <a id="method-clone"></a></p><h3>Method <code>clone()</code></h3> <p>The objects of this class are cloneable with this method.</p><h3>Usage</h3> @@ -193,13 +206,18 @@ value in order to be compatible with mkinfit</p></dd> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> -<span class='no'>mds</span> <span class='kw'><-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>)</div></pre> +<span class='no'>mds</span> <span class='kw'><-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>) +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>mds</span>)</div><div class='output co'>#> <mkinds> with $title: FOCUS A +#> Observed compounds $observed: parent +#> Sampling times $sampling_times: 0, 3, 7, 14, 30, 62, 90, 118 +#> With a maximum of 1 replicates</div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#fields">Fields</a></li> + <li><a href="#see-also">See also</a></li> + <li><a href="#public-fields">Public fields</a></li> <li><a href="#methods">Methods</a></li> <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index d7ba94e1..de1a2410 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -36,7 +36,7 @@ <meta property="og:title" content="Print mkinds objects — print.mkinds" /> -<meta property="og:description" content="Print mkinds objects." /> +<meta property="og:description" content="Print mkinds objects" /> <meta name="twitter:card" content="summary" /> @@ -69,7 +69,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> </span> </div> @@ -133,7 +133,7 @@ </div> <div class="ref-description"> - <p>Print mkinds objects.</p> + <p>Print mkinds objects</p> </div> <pre class="usage"><span class='co'># S3 method for mkinds</span> diff --git a/man/mkinds.Rd b/man/mkinds.Rd index 79eb0167..3bbb1c4b 100644 --- a/man/mkinds.Rd +++ b/man/mkinds.Rd @@ -1,38 +1,43 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/mkinds.R -\docType{class} \name{mkinds} \alias{mkinds} \title{A dataset class for mkin} -\format{An \code{\link{R6Class}} generator object.} \description{ -A dataset class for mkin +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 +provided by this package come as mkinds objects nevertheless. } -\section{Fields}{ +\examples{ +mds <- mkinds$new("FOCUS A", FOCUS_2006_A) +print(mds) -\describe{ \item{list("title")}{A full title for the dataset} +} +\seealso{ +The S3 printing method \code{\link{print.mkinds}} +} +\section{Public fields}{ +\if{html}{\out{<div class="r6-fields">}} +\describe{ +\item{\code{title}}{A full title for the dataset} -\item{list("sampling")}{times The sampling times} +\item{\code{sampling_times}}{The sampling times} -\item{list("time_unit")}{The time unit} +\item{\code{time_unit}}{The time unit} -\item{list("observed")}{Names of the observed compounds} +\item{\code{observed}}{Names of the observed variables} -\item{list("unit")}{The unit of the observations} +\item{\code{unit}}{The unit of the observations} -\item{list("replicates")}{The number of replicates} +\item{\code{replicates}}{The maximum number of replicates per sampling time} -\item{list("data")}{A dataframe with at least the columns name, time and -value in order to be compatible with mkinfit} } +\item{\code{data}}{A data frame with at least the columns name, time +and value in order to be compatible with mkinfit} } - -\examples{ - -mds <- mkinds$new("FOCUS A", FOCUS_2006_A) - +\if{html}{\out{</div>}} } -\keyword{datasets} \section{Methods}{ \subsection{Public methods}{ \itemize{ @@ -43,10 +48,24 @@ mds <- mkinds$new("FOCUS A", FOCUS_2006_A) \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-new"></a>}} \subsection{Method \code{new()}}{ +Create a new mkinds object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{mkinds$new(title = "", data, time_unit = NA, unit = NA)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{title}}{The dataset title} + +\item{\code{data}}{The data} + +\item{\code{time_unit}}{The time unit} + +\item{\code{unit}}{The unit of the observations} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-clone"></a>}} diff --git a/man/print.mkinds.Rd b/man/print.mkinds.Rd index 54dc5a12..51ef3b76 100644 --- a/man/print.mkinds.Rd +++ b/man/print.mkinds.Rd @@ -12,5 +12,5 @@ \item{\dots}{Not used.} } \description{ -Print mkinds objects. +Print mkinds objects } @@ -2,52 +2,37 @@ Loading mkin Testing mkin ✔ | OK F W S | Context ✔ | 2 | Export dataset for reading into CAKE -✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.8 s] +✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.7 s] ✔ | 4 | Calculation of FOCUS chi2 error levels [2.3 s] -✔ | 4 | Fitting the SFORB model [1.7 s] +✔ | 4 | Fitting the SFORB model [1.8 s] ✔ | 5 | Calculation of Akaike weights -✔ | 10 | Confidence intervals and p-values [10.2 s] -✔ | 14 | Error model fitting [40.7 s] +✔ | 10 | Confidence intervals and p-values [10.7 s] +✔ | 14 | Error model fitting [42.8 s] ✔ | 6 | Test fitting the decline of metabolites from their maximum [0.8 s] ✔ | 1 | Fitting the logistic model [1.0 s] ✔ | 1 | Test dataset class mkinds used in gmkin -✖ | 11 1 | Special cases of mkinfit calls [2.3 s] -──────────────────────────────────────────────────────────────────────────────── -test_mkinfit_errors.R:64: failure: We get reproducible output if quiet = FALSE -Results have changed from known value recorded in 'DFOP_FOCUS_C_messages.txt'. -2/165 mismatches -x[84]: "Sum of squared residuals at call 57: 4.364077" -y[84]: "Sum of squared residuals at call 57: 4.364078" - -x[105]: "85.00134 -0.7776046 -4.025878 1.248775 " -y[105]: "85.00135 -0.7776046 -4.025878 1.248775 " -──────────────────────────────────────────────────────────────────────────────── +✔ | 12 | Special cases of mkinfit calls [2.5 s] ✔ | 9 | mkinmod model generation and printing [0.2 s] -✔ | 3 | Model predictions with mkinpredict [0.3 s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.3 s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s] +✔ | 3 | Model predictions with mkinpredict [0.4 s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.4 s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3 s] ✔ | 3 | Summary -✖ | 10 1 | Plotting [0.6 s] -──────────────────────────────────────────────────────────────────────────────── -test_plots_summary_twa.R:118: failure: Plotting mkinfit and mmkin objects is reproducible -Figures don't match: plot-errmod-with-sfo-lin-a-obs.svg - -──────────────────────────────────────────────────────────────────────────────── +✔ | 11 | Plotting [0.6 s] ✔ | 4 | AIC calculation ✔ | 2 | Residuals extracted from mkinfit models -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.6 s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.7 s] ✔ | 1 | Summaries of old mkinfit objects -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.4 s] -✔ | 7 1 | Hypothesis tests [33.6 s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.7 s] +✔ | 7 1 | Hypothesis tests [35.7 s] ──────────────────────────────────────────────────────────────────────────────── test_tests.R:60: skip: We can do a likelihood ratio test using an update specification Reason: This errors out if called by testthat while it works in a normal R session ──────────────────────────────────────────────────────────────────────────────── ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 117.3 s +Duration: 123.0 s -OK: 136 -Failed: 2 +OK: 138 +Failed: 0 Warnings: 0 Skipped: 1 |