diff options
Diffstat (limited to 'R/mmkin.R')
| -rw-r--r-- | R/mmkin.R | 113 |
1 files changed, 91 insertions, 22 deletions
@@ -1,24 +1,65 @@ -# Copyright (C) 2015,2019 Johannes Ranke -# Contact: jranke@uni-bremen.de -# The summary function is an adapted and extended version of summary.modFit -# from the FME package, v 1.1 by Soetart and Petzoldt, which was in turn -# inspired by summary.nls.lm - -# 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/> - +#' Fit one or more kinetic models with one or more state variables to one or +#' more datasets +#' +#' This function calls \code{\link{mkinfit}} on all combinations of models and +#' datasets specified in its first two arguments. +#' +#' @param models Either a character vector of shorthand names like +#' \code{c("SFO", "FOMC", "DFOP", "HS", "SFORB")}, or an optionally named +#' list of \code{\link{mkinmod}} objects. +#' @param datasets An optionally named list of datasets suitable as observed +#' data for \code{\link{mkinfit}}. +#' @param cores The number of cores to be used for multicore processing. This +#' is only used when the \code{cluster} argument is \code{NULL}. On Windows +#' machines, cores > 1 is not supported, you need to use the \code{cluster} +#' argument to use multiple logical processors. +#' @param cluster A cluster as returned by \code{\link{makeCluster}} to be used +#' for parallel execution. +#' @param \dots Further arguments that will be passed to \code{\link{mkinfit}}. +#' @importFrom parallel mclapply parLapply detectCores +#' @return A matrix of \code{\link{mkinfit}} objects that can be indexed using +#' the model and dataset names as row and column indices. +#' @author Johannes Ranke +#' @seealso \code{\link{[.mmkin}} for subsetting, \code{\link{plot.mmkin}} for +#' plotting. +#' @keywords optimize +#' @examples +#' +#' \dontrun{ +#' m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"), +#' M1 = mkinsub("SFO", "M2"), +#' M2 = mkinsub("SFO"), use_of_ff = "max") +#' +#' m_synth_FOMC_lin <- mkinmod(parent = mkinsub("FOMC", "M1"), +#' M1 = mkinsub("SFO", "M2"), +#' M2 = mkinsub("SFO"), use_of_ff = "max") +#' +#' models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin) +#' datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data) +#' names(datasets) <- paste("Dataset", 1:3) +#' +#' time_default <- system.time(fits.0 <- mmkin(models, datasets, quiet = TRUE)) +#' time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) +#' +#' time_default +#' time_1 +#' +#' endpoints(fits.0[["SFO_lin", 2]]) +#' +#' # plot.mkinfit handles rows or columns of mmkin result objects +#' plot(fits.0[1, ]) +#' plot(fits.0[1, ], obs_var = c("M1", "M2")) +#' plot(fits.0[, 1]) +#' # Use double brackets to extract a single mkinfit object, which will be plotted +#' # by plot.mkinfit and can be plotted using plot_sep +#' plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE) +#' plot_sep(fits.0[[1, 1]]) +#' # Plotting with mmkin (single brackets, extracting an mmkin object) does not +#' # allow to plot the observed variables separately +#' plot(fits.0[1, 1]) +#' } +#' +#' @export mmkin mmkin <- function(models = c("SFO", "FOMC", "DFOP"), datasets, cores = round(detectCores()/2), cluster = NULL, ...) { @@ -66,7 +107,35 @@ mmkin <- function(models = c("SFO", "FOMC", "DFOP"), datasets, return(results) } -"[.mmkin" <- function(x, i, j, ..., drop = FALSE) { +#' Subsetting method for mmkin objects +#' +#' Subsetting method for mmkin objects. +#' +#' @param x An \code{\link{mmkin} object} +#' @param i Row index selecting the fits for specific models +#' @param j Column index selecting the fits to specific datasets +#' @param ... Not used, only there to satisfy the generic method definition +#' @param drop If FALSE, the method always returns an mmkin object, otherwise +#' either a list of mkinfit objects or a single mkinfit object. +#' @return An object of class \code{\link{mmkin}}. +#' @author Johannes Ranke +#' @rdname Extract.mmkin +#' @examples +#' +#' # Only use one core, to pass R CMD check --as-cran +#' fits <- mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C), +#' cores = 1, quiet = TRUE) +#' fits["FOMC", ] +#' fits[, "B"] +#' fits["SFO", "B"] +#' +#' head( +#' # This extracts an mkinfit object with lots of components +#' fits[["FOMC", "B"]] +#' ) +#' +#' @export +`[.mmkin` <- function(x, i, j, ..., drop = FALSE) { class(x) <- NULL x_sub <- x[i, j, drop = drop] if (!drop) class(x_sub) <- "mmkin" |