1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
|
#' A dataset class for mkin
#'
#' @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
#' @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
self$sampling_times <- sort(unique(data$time))
self$time_unit <- time_unit
self$observed <- unique(data$name)
self$unit <- unit
self$replicates <- max(by(data, list(data$name, data$time), nrow))
if (is.null(data$override)) data$override <- NA
if (is.null(data$err)) data$err <- 1
self$data <- data
}
)
)
#' Print mkinds objects
#'
#' @param x An \code{\link{mkinds}} object.
#' @param \dots Not used.
#' @export
print.mkinds <- function(x, ...) {
cat("<mkinds> with $title: ", x$title, "\n")
cat("Observed compounds $observed: ", paste(x$observed, collapse = ", "), "\n")
cat("Sampling times $sampling_times: ", paste(x$sampling_times, collapse = ", "), "\n")
cat("With a maximum of ", x$replicates, " replicates\n")
if (!is.na(x$time_unit)) cat("Time unit: ", x$time_unit, "\n")
if (!is.na(x$unit)) cat("Observation unit: ", x$unit, "\n")
}
|
