mmkin: Fit one or more kinetic models with one or more state variables to one or more datasets

Description

This function calls mkinfit on all combinations of models and datasets specified in its first two arguments.

Usage

mmkin(
  models = c("SFO", "FOMC", "DFOP"),
  datasets,
  cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(),
  cluster = NULL,
  ...
)
# S3 method for mmkin
print(x, ...)

Value

A two-dimensional array of mkinfit

objects and/or try-errors that can be indexed using the model names for the first index (row index) and the dataset names for the second index (column index).

Arguments

models: Either a character vector of shorthand names like c("SFO", "FOMC", "DFOP", "HS", "SFORB"), or an optionally named list of mkinmod objects.
datasets: An optionally named list of datasets suitable as observed data for mkinfit.
cores: The number of cores to be used for multicore processing. This is only used when the cluster argument is NULL. On Windows machines, cores > 1 is not supported, you need to use the cluster argument to use multiple logical processors. Per default, all cores detected by parallel::detectCores() are used, except on Windows where the default is 1.
cluster: A cluster as returned by makeCluster to be used for parallel execution.
...: Not used.
x: An mmkin object.

Author

Johannes Ranke

Examples

Run this code


if (FALSE) {
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])

# On Windows, we can use multiple cores by making a cluster first
cl <- parallel::makePSOCKcluster(12)
f <- mmkin(c("SFO", "FOMC", "DFOP"),
  list(A = FOCUS_2006_A, B = FOCUS_2006_B, C = FOCUS_2006_C, D = FOCUS_2006_D),
  cluster = cl, quiet = TRUE)
print(f)
# We get false convergence for the FOMC fit to FOCUS_2006_A because this
# dataset is really SFO, and the FOMC fit is overparameterised
parallel::stopCluster(cl)
}