#' 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
#' @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
#'
#' @rdname mkinds
#' @param x An [mkinds] object.
#' @param data Should the data be printed?
#' @param \dots Not used.
#' @export
print.mkinds <- function(x, data = FALSE, ...) {
cat("<mkinds> with $title: ", x$title, "\n")
cat("Observed compounds $observed: ", paste(x$observed, collapse = ", "), "\n")
cat("Sampling times $sampling_times:\n")
cat(paste(x$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$unit, "\n")
if (data) print(mkin_long_to_wide(x$data))
}
#' A class for dataset groups for mkin
#'
#' @description
#' A container for working with datasets that share at least one compound,
#' so that combined evaluations are desirable.
#'
#' Time normalisation factors are initialised with a value of 1 for each
#' dataset if no data are supplied.
#'
#' @examples
#'
#' mdsg <- mkindsg$new("Experimental X", experimental_data_for_UBA_2019[6:10])
#' print(mdsg)
#' print(mdsg, verbose = TRUE)
#' print(mdsg, verbose = TRUE, data = TRUE)
#'
#' @export
mkindsg <- R6Class("mkindsg",
public = list(
#' @field title A title for the dataset group
title = NULL,
#' @field ds A list of mkinds objects
ds = NULL,
#' @field observed_n Occurrence counts of compounds in datasets
observed_n = NULL,
#' @field f_time_norm Time normalisation factors
f_time_norm = NULL,
#' @field meta A data frame with a row for each dataset,
#' containing additional information in the form
#' of categorical data (factors) or numerical data
#' (e.g. temperature, moisture,
#' or covariates like soil pH).
meta = NULL,
#' @description
#' Create a new mkindsg object
#' @param title The title
#' @param ds A list of mkinds objects
#' @param f_time_norm Time normalisation factors
#' @param meta The meta data
initialize = function(title = "", ds,
f_time_norm = rep(1, length(ds)), meta)
{
self$title <- title
if (all(sapply(ds, inherits, "mkinds"))) {
self$ds <- ds
} else {
stop("Please supply a list of mkinds objects")
}
all_observed <- unlist(lapply(ds, function(x) x$observed))
observed <- factor(all_observed, levels = unique(all_observed))
self$observed_n <- table(observed)
names(dimnames(self$observed_n)) <- NULL
self$f_time_norm <- f_time_norm
if (!missing(meta)) {
rownames(meta) <- lapply(ds, function(x) x$title)
self$meta <- meta
}
}
)
)
#' Print mkindsg objects
#'
#' @rdname mkindsg
#' @param x An [mkindsg] object.
#' @param verbose Should the mkinds objects be printed?
#' @param data Should the mkinds objects be printed with their data?
#' @param \dots Not used.
#' @export
print.mkindsg <- function(x, data = FALSE, verbose = data, ...) {
cat("<mkindsg> holding", length(x$ds), "mkinds objects\n")
cat("Title $title: ", x$title, "\n")
cat("Occurrence of observed compounds $observed_n:\n")
print(x$observed_n)
if (any(x$f_time_norm != 1)) {
cat("Time normalisation factors $f_time_norm:\n")
print(x$f_time_norm)
}
if (!is.null(x$meta)) {
cat("Meta information $meta:\n")
print(x$meta)
}
if (verbose) {
cat("\nDatasets $ds:")
for (ds in x$ds) {
cat("\n")
print(ds, data = data)
}
}
}
