From 64a476750ff57f4c612620bd58cc4ac42812e185 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 31 Mar 2020 09:52:19 +0200 Subject: Use inline documentation for R6 class mkinds --- R/mkinds.R | 53 ++++++++++++++++++--------------- docs/reference/mkinds.html | 64 +++++++++++++++++++++++++--------------- docs/reference/print.mkinds.html | 6 ++-- man/mkinds.Rd | 55 +++++++++++++++++++++++----------- man/print.mkinds.Rd | 2 +- test.log | 45 ++++++++++------------------ 6 files changed, 126 insertions(+), 99 deletions(-) diff --git a/R/mkinds.R b/R/mkinds.R index a66adb14..d6f296bf 100644 --- a/R/mkinds.R +++ b/R/mkinds.R @@ -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 @@ - + @@ -133,36 +136,36 @@
-

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.

-

Format

+

See also

-

An R6Class generator object.

-

Fields

+

The S3 printing method print.mkinds

+

Public fields

- - - -
-
list("title")

A full title for the dataset

+

+
title

A full title for the dataset

-
list("sampling")

times The sampling times

+
sampling_times

The sampling times

-
list("time_unit")

The time unit

+
time_unit

The time unit

-
list("observed")

Names of the observed compounds

+
observed

Names of the observed variables

-
list("unit")

The unit of the observations

+
unit

The unit of the observations

-
list("replicates")

The number of replicates

+
replicates

The maximum number of replicates per sampling time

-
list("data")

A dataframe with at least the columns name, time and -value in order to be compatible with mkinfit

-
+
data

A data frame with at least the columns name, time +and value in order to be compatible with mkinfit

+

Methods

@@ -174,10 +177,20 @@ value in order to be compatible with mkinfit

Method new()

- -

Usage

+

Create a new mkinds object

Usage

mkinds$new(title = "", data, time_unit = NA, unit = NA)

+

Arguments

+

+
title

The dataset title

+ +
data

The data

+ +
time_unit

The time unit

+ +
unit

The unit of the observations

+ +

Method clone()

The objects of this class are cloneable with this method.

Usage

@@ -193,13 +206,18 @@ value in order to be compatible with mkinfit

Examples


-mds <- mkinds$new("FOCUS A", FOCUS_2006_A)
+mds <- mkinds$new("FOCUS A", FOCUS_2006_A) +print(mds)
#> <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
+
@@ -133,7 +133,7 @@
-

Print mkinds objects.

+

Print mkinds objects

# S3 method for mkinds
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{
}}
+\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$new("FOCUS A", FOCUS_2006_A)
-
+\if{html}{\out{
}}
 }
-\keyword{datasets}
 \section{Methods}{
 \subsection{Public methods}{
 \itemize{
@@ -43,10 +48,24 @@ mds <- mkinds$new("FOCUS A", FOCUS_2006_A)
 \if{html}{\out{
}}
 \if{html}{\out{}}
 \subsection{Method \code{new()}}{
+Create a new mkinds object
 \subsection{Usage}{
 \if{html}{\out{
}}\preformatted{mkinds$new(title = "", data, time_unit = NA, unit = NA)}\if{html}{\out{
}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{
}}
+\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{
}}
+}
 }
 \if{html}{\out{
}}
 \if{html}{\out{}}
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
 }
diff --git a/test.log b/test.log
index 2db18301..77130814 100644
--- a/test.log
+++ b/test.log
@@ -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
-- 
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