#' 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) } } }