From a77a10ea6c607346778ba0700b3b66ac393101a2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 27 May 2020 06:06:08 +0200 Subject: Create up to date pkgdown docs in development mode --- docs/dev/reference/mmkin.html | 271 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 271 insertions(+) create mode 100644 docs/dev/reference/mmkin.html (limited to 'docs/dev/reference/mmkin.html') diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html new file mode 100644 index 00000000..1b5c1592 --- /dev/null +++ b/docs/dev/reference/mmkin.html @@ -0,0 +1,271 @@ + + + + + + + + +Fit one or more kinetic models with one or more state variables to one or +more datasets — mmkin • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+ +
+
+
+

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

+ Source: R/mmkin.R + +
+ +
+

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

+
+ + 
mmkin(
+  models = c("SFO", "FOMC", "DFOP"),
+  datasets,
+  cores = detectCores(),
+  cluster = NULL,
+  ...
+)
+ +

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.

cluster

A cluster as returned by makeCluster to be used +for parallel execution.

...

Further arguments that will be passed to mkinfit.

+ +

Value

+ +

A two-dimensional array of mkinfit +objects that can be indexed using the model names for the first index (row index) +and the dataset names for the second index (column index).

+

See also

+ +

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

+ +

Examples

+ 

+# \dontrun{
+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))
#> Warning: Optimisation did not converge:
+#> false convergence (8)

+time_default
#>    user  system elapsed 
+#>   4.516   0.456   1.976 
time_1
#>    user  system elapsed 
+#>   5.957   0.001   5.961 

+endpoints(fits.0[["SFO_lin", 2]])
#> $ff
+#>   parent_M1 parent_sink       M1_M2     M1_sink 
+#>   0.7340479   0.2659521   0.7505687   0.2494313 
+#> 
+#> $distimes
+#>              DT50       DT90
+#> parent  0.8777688   2.915885
+#> M1      2.3257457   7.725960
+#> M2     33.7200848 112.015697
+#> 

+# 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])
# }
+
+
+
+ +
+ + + +
+ + + + + + + + -- cgit v1.2.1