diff options
Diffstat (limited to 'R/mkinds.R')
| -rw-r--r-- | R/mkinds.R | 117 |
1 files changed, 109 insertions, 8 deletions
@@ -1,5 +1,5 @@ #' 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 @@ -7,12 +7,11 @@ #' 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( @@ -62,15 +61,117 @@ mkinds <- R6Class("mkinds", ) #' Print mkinds objects -#' -#' @param x An \code{\link{mkinds}} object. +#' +#' @rdname mkinds +#' @param x An [mkinds] object. +#' @param data Should the data be printed? #' @param \dots Not used. #' @export -print.mkinds <- function(x, ...) { +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 $sampling_times: ", paste(x$sampling_times, 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$f_time_norm <- f_time_norm + + if (!missing(meta)) { + self$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("Occurrene 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) + } + } } |