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

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

mmkin(models, datasets,
      cores = round(detectCores()/2), cluster = NULL, ...)

Arguments

models	Either a character vector of shorthand names ("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.
cluster	A cluster as returned by makeCluster to be used for parallel execution.
…	Further arguments that will be passed to mkinfit.

Value

A matrix of mkinfit objects that can be indexed using the model and dataset names as row and column indices.

See also

[.mmkin for subsetting, plot.mmkin for plotting.

Examples

m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
                           M1 = mkinsub("SFO", "M2"),
                           M2 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

m_synth_FOMC_lin <- mkinmod(parent = mkinsub("FOMC", "M1"),
                            M1 = mkinsub("SFO", "M2"),
                            M2 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

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
#>        User      System verstrichen 
#>       0.040       0.047       7.314 
time_1
#>        User      System verstrichen 
#>      22.751       0.000      22.766 

endpoints(fits.0[["SFO_lin", 2]])
#> $ff
#>   parent_M1 parent_sink       M1_M2     M1_sink 
#>   0.7340480   0.2659520   0.7505686   0.2494314 
#> 
#> $SFORB
#> logical(0)
#> 
#> $distimes
#>              DT50       DT90
#> parent  0.8777689   2.915885
#> M1      2.3257453   7.725959
#> M2     33.7200874 112.015706
#> 

# 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])