From 575fcacaa33076de97f41a79afb37efb97ca82e0 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 30 Mar 2020 21:43:10 +0200 Subject: Static documentation rebuilt by pkgdown --- docs/reference/mkinds.html | 31 +++++++++++++++++++++++++++++-- 1 file changed, 29 insertions(+), 2 deletions(-) (limited to 'docs/reference/mkinds.html') diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 386c00d7..c1cdcf99 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -69,7 +69,7 @@ mkin - 0.9.49.6 + 0.9.49.9 @@ -136,7 +136,6 @@

A dataset class for mkin

- 
mkinds

Format

@@ -164,6 +163,33 @@ value in order to be compatible with mkinfit

+

Methods

+ + +

Public methods

+ + +

+

Method new()

+ +

Usage

+

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

+ +

+

Method clone()

+

The objects of this class are cloneable with this method.

Usage

+

mkinds$clone(deep = FALSE)

+ +

Arguments

+

+
deep

Whether to make a deep clone.

+ +

+ +

Examples


@@ -174,6 +200,7 @@ value in order to be compatible with mkinfit

     
 
-- 
cgit v1.2.3


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(-)

(limited to 'docs/reference/mkinds.html')

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
-- 
cgit v1.2.3