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| -rw-r--r-- | R/mkinds.R | 65 | ||||
| -rw-r--r-- | R/plot.mkinfit.R | 2 |
2 files changed, 67 insertions, 0 deletions
diff --git a/R/mkinds.R b/R/mkinds.R new file mode 100644 index 00000000..17d40875 --- /dev/null +++ b/R/mkinds.R @@ -0,0 +1,65 @@ +# Copyright (C) 2015 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 +#' @examples 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 = 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)) + 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 units: ", x$time_units, "\n") + if (!is.na(x$unit)) cat("Observation units: ", x$units, "\n") +} diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index f8ee600e..6ca7e531 100644 --- a/R/plot.mkinfit.R +++ b/R/plot.mkinfit.R @@ -77,8 +77,10 @@ plot.mkinfit <- function(x, fit = x, matlines(out$time, out[obs_vars], col = col_obs[obs_vars], lty = lty_obs[obs_vars]) if (legend == TRUE) { legend_names = lapply(names(fit$mkinmod$spec), function(x) { + if (!is.null(fit$mkinmod$spec[[x]]$full_name)) if (is.na(fit$mkinmod$spec[[x]]$full_name)) x else fit$mkinmod$spec[[x]]$full_name + else x }) legend(lpos, inset= inset, legend = legend_names, col = col_obs[obs_vars], pch = pch_obs[obs_vars], lty = lty_obs[obs_vars]) |