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-rw-r--r--R/mkinds.R117
1 files changed, 109 insertions, 8 deletions
diff --git a/R/mkinds.R b/R/mkinds.R
index d6f296bf..0e970694 100644
--- a/R/mkinds.R
+++ b/R/mkinds.R
@@ -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)
+ }
+ }
}

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