multistart: Perform a hierarchical model fit with multiple starting...

In mkin: Kinetic Evaluation of Chemical Degradation Data

Perform a hierarchical model fit with multiple starting values

Description

The purpose of this method is to check if a certain algorithm for fitting nonlinear hierarchical models (also known as nonlinear mixed-effects models) will reliably yield results that are sufficiently similar to each other, if started with a certain range of reasonable starting parameters. It is inspired by the article on practical identifiabiliy in the frame of nonlinear mixed-effects models by Duchesne et al (2021).

Usage

multistart(
  object,
  n = 50,
  cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(),
  cluster = NULL,
  ...
)

## S3 method for class 'saem.mmkin'
multistart(object, n = 50, cores = 1, cluster = NULL, ...)

## S3 method for class 'multistart'
print(x, ...)

best(object, ...)

## Default S3 method:
best(object, ...)

which.best(object, ...)

## Default S3 method:
which.best(object, ...)

Arguments

object	The fit object to work with
n	How many different combinations of starting parameters should be used?
cores	How many fits should be run in parallel (only on posix platforms)?
cluster	A cluster as returned by parallel::makeCluster to be used for parallel execution.
...	Passed to the update function.
x	The multistart object to print

Value

A list of saem.mmkin objects, with class attributes 'multistart.saem.mmkin' and 'multistart'.

The object with the highest likelihood

The index of the object with the highest likelihood

References

Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical identifiability in the frame of nonlinear mixed effects models: the example of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478. doi: 10.1186/s12859-021-04373-4.

See Also

parplot, llhist

Examples

## Not run: 
library(mkin)
dmta_ds <- lapply(1:7, function(i) {
  ds_i <- dimethenamid_2018$ds[[i]]$data
  ds_i[ds_i$name == "DMTAP", "name"] <-  "DMTA"
  ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i]
  ds_i
})
names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title)
dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]])
dmta_ds[["Elliot 1"]] <- dmta_ds[["Elliot 2"]] <- NULL

f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE)
f_saem_full <- saem(f_mmkin)
f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16)
parplot(f_saem_full_multi, lpos = "topleft", las = 2)
illparms(f_saem_full)

f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2")
illparms(f_saem_reduced)
# On Windows, we need to create a PSOCK cluster first and refer to it
# in the call to multistart()
library(parallel)
cl <- makePSOCKcluster(12)
f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cluster = cl)
parplot(f_saem_reduced_multi, lpos = "topright", ylim = c(0.5, 2), las = 2)
stopCluster(cl)

## End(Not run)

mkin documentation built on April 12, 2025, 2:24 a.m.