setCov: Set the covariance type based on prior calculated covariances

In nlmixr2est: Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines

Set the covariance type based on prior calculated covariances

Description

Switches a completed fit's covariance to method. A previously computed covariance is re-installed from the cache; otherwise it is recomputed at the converged estimates: "r,s"/"r"/"s" and "analytic" on a zero-iteration FOCEI model, and "sa" (SAEM Louis FIM) / "imp" (importance-sampling Monte-Carlo) via the decoupled recompute engine (the latter two require a mixed-effects fit). When a covariance cannot be computed it is left unchanged (it is never silently downgraded to "r,s").

Usage

setCov(fit, method, ...)

## Default S3 method:
setCov(fit, method, ...)

## S3 method for class 'analytic'
setCov(fit, method, ...)

## S3 method for class ''r,s''
setCov(fit, method, control = rsControl(), ...)

## S3 method for class 'r'
setCov(fit, method, control = rsControl(), ...)

## S3 method for class 's'
setCov(fit, method, control = rsControl(), ...)

## S3 method for class 'sa'
setCov(fit, method, control = saControl(), ...)

## S3 method for class 'imp'
setCov(fit, method, control = impCovControl(), ...)

Arguments

fit	nlmixr2 fit
method	covariance method (see the covMethod argument of the control options for the choices)
...	arguments passed to the covariance method
control	options for the covariance method itself, only needed to change its defaults: rsControl() for "r,s", "r" and "s", saControl() for "sa" and impCovControl() for "imp"

Details

Every focei covariance comes in two shapes (see covFull in foceiControl()), and both are named: "r,s", "r", "s" and "analytic" are the structural-theta block, while "r,s (full)", "r (full)", "s (full)" and "analytic (full)" are the full theta + residual sigma + Omega matrix. A focei fit computes both and caches the one it does not install, so swapping between them costs nothing. The shapes are not submatrices of one another on the finite-difference path – "s" inverts the theta block of the cross-product while "s (full)" takes the theta block of the full inverse, which also carries the Omega estimation uncertainty – so the standard errors differ. On the analytic path the assembly is always full and "analytic" is a submatrix of "analytic (full)", so the theta standard errors agree.

fit$covMethod names the installed covariance and names(fit$covList) the cached alternatives (the fit print shows both).

Value

Fit object with covariance updated

Adding a covariance method

setCov() is an S3 generic dispatched on method (without any " (full)" suffix), so another package (for example SIR or a bootstrap) can add a covariance by registering a method:

# registered with S3method(nlmixr2est::setCov, sir) in NAMESPACE
setCov.sir <- function(fit, method, control = sirControl(), ...) {
  # compute on the estimation scale, named like fit$cov
  mySirCovariance(fit, control)
}

A method that has options declares its own control holding only those options, so setCov(fit, "sir") uses the defaults and setCov(fit, "sir", control = sirControl(...)) changes them. The method receives the fit and method (carrying dispatch classes; use unclass(method) for the plain name) and either returns a named covariance matrix, which setCov() checks for positive definiteness and installs as method (updating the standard errors and keeping the prior covariance in fit$covList), or installs the covariance itself and returns NULL. A mixture fit's matrix is rotated onto the probability scale unless it carries attr(, "mixRotated") set to TRUE. A method that cannot compute the covariance should stop(). setCovAllMethods() lists the available methods.

A method's options are recorded under the key setCovOptions() gives its control, by default the control itself. A covariance that depends on other state on the fit – one seeded from another covariance, say – adds a setCovOptions() method for its control class that puts that state in the key. A package can also let an already-computed result be installed with setCov(fit) <- result by adding a setCovValue() method for the result's class.

Each covariance remembers the options it was computed with (in fit$env$covOptions). A covariance already on the fit is reinstalled from fit$covList only when the requested options – the supplied control, or the method's default one – are the same; otherwise it is recomputed. A covariance computed during estimation used the fit's own settings.

Author(s)

Matt Fidler

See Also

foceiControl(), saemControl()

nlmixr2est documentation built on Sept. 20, 2026, 9:08 a.m.