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# Copyright (C) 2015,2018 Johannes Ranke
# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
# mkin is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>
#' A dataset class for mkin
#'
#' @docType class
#' @importFrom R6 R6Class
#' @export
#' @format An \code{\link{R6Class}} generator object.
#' @field title A full title for the dataset
#' @field sampling times The sampling times
#' @field time_unit The time unit
#' @field observed Names of the observed compounds
#' @field unit The unit of the observations
#' @field replicates The number of replicates
#' @field data A dataframe with at least the columns name, time and value
#' in order to be compatible with mkinfit
#' @example inst/examples/mkinds.R
mkinds <- R6Class("mkinds",
public = list(
title = NULL,
sampling_times = NULL,
time_unit = NULL,
observed = NULL,
unit = NULL,
replicates = NULL,
data = NULL,
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
}
)
)
#' @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")
}
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