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| -rw-r--r-- | NEWS.md | 4 | ||||
| -rw-r--r-- | R/mmkin.R | 46 | ||||
| -rw-r--r-- | man/mmkin.Rd | 64 |
3 files changed, 113 insertions, 1 deletions
@@ -1,6 +1,8 @@ # CHANGES in mkin VERSION 0.9-39 - +## MAJOR CHANGES + +- New function `mmkin()`: This function takes a character vector of model shorthand names, or alternatively a list of mkinmod models, as well as a list of dataset as main arguments. It returns a matrix of mkinfit objects, with a row for each model and a column for each dataset. # CHANGES in mkin VERSION 0.9-38 diff --git a/R/mmkin.R b/R/mmkin.R new file mode 100644 index 00000000..fe9db194 --- /dev/null +++ b/R/mmkin.R @@ -0,0 +1,46 @@ +mmkin <- function(models = c("SFO", "FOMC", "DFOP"), datasets, + cores = round(detectCores()/2), cluster = NULL, ...) +{ + parent_models_available = c("SFO", "FOMC", "DFOP", "HS", "SFORB", "IORE") + n.m <- length(models) + n.d <- length(datasets) + n.fits <- n.m * n.d + fit_indices <- matrix(1:n.fits, ncol = n.d) + + # Check models and define their names + if (!all(sapply(models, function(x) inherits(x, "mkinmod")))) { + if (!all(models %in% parent_models_available)) { + stop("Please supply models as a list of mkinmod objects or a vector combined of\n ", + paste(parent_models_available, collapse = ", ")) + } else { + names(models) <- models + } + } else { + if (is.null(names(models))) names(models) <- as.character(1:n.m) + } + + # Check datasets and define their names + if (is.null(names(datasets))) names(datasets) <- as.character(1:n.d) + + # Define names for fit index + dimnames(fit_indices) <- list(model = names(models), + dataset = names(datasets)) + + + fit_function <- function(fit_index) { + w <- which(fit_indices == fit_index, arr.ind = TRUE) + model_index <- w[1] + dataset_index <- w[2] + mkinfit(models[[model_index]], datasets[[dataset_index]], ...) + } + + if (is.null(cluster)) { + results <- mclapply(as.list(1:n.fits), fit_function, mc.cores = cores) + } else { + results <- parLapply(cluster, list(1:n.fit), fit_function) + } + + attributes(results) <- attributes(fit_indices) + class(results) <- "mmkin" + return(results) +} diff --git a/man/mmkin.Rd b/man/mmkin.Rd new file mode 100644 index 00000000..64e7ae27 --- /dev/null +++ b/man/mmkin.Rd @@ -0,0 +1,64 @@ +\name{mmkin} +\alias{mmkin} +\title{ + Fit one or more kinetic models with one or more state variables to one or more datasets +} +\description{ + This code calls \code{\link{mkinfit}} on each combination of model and dataset + given in its first two arguments. +} +\usage{ +mmkin(models, datasets, + cores = round(detectCores()/2), cluster = NULL, ...) +} +\arguments{ + \item{models}{ + Either a character vector of shorthand names ("SFO", "FOMC", "DFOP", + "HS", "SFORB"), or an optionally named list of \code{\link{mkinmod}} + objects. + } + \item{datasets}{ + An optionally named list of datasets suitable as observed data for + \code{\link{mkinfit}}. + } + \item{cores}{ + The number of cores to be used for multicore processing. This is only + used when the \code{cluster} argument is \code{NULL}. + } + \item{cluster}{ + A cluster as returned by \code{link{makeCluster}} to be used for parallel + execution. + } + \item{\dots}{ + Further arguments that will be passed to \code{\link{mkinfit}}. + } +} +\value{ + A matrix of "mkinfit" objects that can be indexed using the + model and dataset names as row and column indices. +} +\author{ + Johannes Ranke +} +\examples{ +\dontrun{ +m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"), + M1 = list(type = "SFO", to = "M2"), + M2 = list(type = "SFO"), use_of_ff = "max") + +m_synth_FOMC_lin <- mkinmod(parent = list(type = "FOMC", to = "M1"), + M1 = list(type = "SFO", to = "M2"), + M2 = list(type = "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) + +time_default <- system.time(fits <- mmkin(models, datasets)) +time_1 <- system.time(fits.1 <- mmkin(models, datasets, cores = 1)) + +time_default +time_1 + +endpoints(fits[["SFO_lin", 2]]) +} +\keyword{ optimize } |