patch_condn

<a href="https://lifecycle.r-lib.org/articles/stages.html#experimental"><img src="figures/lifecycle-experimental.svg?package=xpose.xtras&version=0.2.2" alt="[Experimental]"></a>
Bugfix for <code>xpose:::sum_condn</code>, the internal function <code>xpose</code> uses to
populate the <code>'condn'</code> (condition number) entry of <code>xpdb$summary</code>.
For NONMEM runs with more than one estimation method (e.g. <code>SAEM</code> followed
by importance sampling), the <code>.lst</code> file contains more than one
<code>EIGENVALUES OF COR MATRIX OF ESTIMATE</code> block. <code>xpose</code> always uses the
first block found, which is not necessarily from the final estimation
method, so the reported condition number can be wrong. This patch instead
uses the last block, matching the value reported by NONMEM-adjacent
tools such as PsN's <code>sumo</code>.
<code>xpose:::sum_condn()</code> itself (not this function) is also where a multi-
method run with more than one <code>EIGENVALUES OF COR</code> block raises "numerical
expression has ... elements: only the first used" -- it runs automatically
inside <code>xpose::xpose_data()</code>, before <code>patch_condn()</code> gets a chance to
run, so that warning is expected and cannot be suppressed from here; this
function only fixes the resulting <code>'condn'</code> value afterward.

Adding some at-present missing functionality, or functions
unlikely to be added to the base 'xpose' package.  This includes some
diagnostic plots that have been missing in translation from 'xpose4',
but also some useful features that truly extend the capabilities of what
can be done with 'xpose'. These extensions include the concept of a set of
'xpose' objects, and diagnostics for likelihood-based models.

John Prybylski

xpose.xtras

Extra Functionality for the 'xpose' Package

patch_condn function

<dl><dt>xpdb</dt>
<dd>An <code>xpose_data</code> or <code>xp_xtras</code> object.</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#experimental'><img src='figures/lifecycle-experimental.svg' alt='[Experimental]' /></a>
Bugfix for <code>xpose:::sum_condn</code>, the internal function <code>xpose</code> uses to
populate the <code>'condn'</code> (condition number) entry of <code>xpdb$summary</code>.
For NONMEM runs with more than one estimation method (e.g. <code>SAEM</code> followed
by importance sampling), the <code>.lst</code> file contains more than one
<code>EIGENVALUES OF COR MATRIX OF ESTIMATE</code> block. <code>xpose</code> always uses the
first block found, which is not necessarily from the final estimation
method, so the reported condition number can be wrong. This patch instead
uses the last block, matching the value reported by NONMEM-adjacent
tools such as PsN's <code>sumo</code>.
<code>xpose:::sum_condn()</code> itself (not this function) is also where a multi-
method run with more than one <code>EIGENVALUES OF COR</code> block raises "numerical
expression has ... elements: only the first used" -- it runs automatically
inside <code>xpose::xpose_data()</code>, before <code>patch_condn()</code> gets a chance to
run, so that warning is expected and cannot be suppressed from here; this
function only fixes the resulting <code>'condn'</code> value afterward.

Patch condition number extraction — patch_condn

<dl>

<dt>xpdb</dt>
<dd>An <code>xpose_data</code> or <code>xp_xtras</code> object.</dd>

</dl>

patch_condn: Patch condition number extraction

Description

Usage

Value

Arguments

Examples