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authorJohannes Ranke <jranke@uni-bremen.de>2021-09-27 20:10:01 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2021-09-27 20:10:01 +0200
commit5c15ef747568b3a9a9c094b6aa546dc80e3aa87a (patch)
tree70f86619437fb8f1bc1f144b847fc4dacbcba128 /docs/dev/reference
parent047d048b89e167fb354b45cd7c6b719b9f4cdd28 (diff)
intervals() methods, more DFOP/tc variants
Diffstat (limited to 'docs/dev/reference')
-rw-r--r--docs/dev/reference/Rplot001.pngbin1011 -> 43845 bytes
-rw-r--r--docs/dev/reference/index.html18
-rw-r--r--docs/dev/reference/intervals.nlmixr.mmkin.html203
-rw-r--r--docs/dev/reference/intervals.saem.mmkin.html205
-rw-r--r--docs/dev/reference/nlmixr.mmkin.html33
-rw-r--r--docs/dev/reference/reexports.html6
6 files changed, 446 insertions, 19 deletions
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index 17a35806..c26c864f 100644
--- a/docs/dev/reference/Rplot001.png
+++ b/docs/dev/reference/Rplot001.png
Binary files differ
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index d5ec387a..092e35c8 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -370,6 +370,24 @@ of an mmkin object</p></td>
<p><code><a href="mixed.html">mixed()</a></code> <code><a href="mixed.html">print(<i>&lt;mixed.mmkin&gt;</i>)</a></code> </p>
</td>
<td><p>Create a mixed effects model from an mmkin row object</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="reexports.html">reexports</a></code> </p>
+ </td>
+ <td><p>Objects exported from other packages</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="intervals.saem.mmkin.html">intervals(<i>&lt;saem.mmkin&gt;</i>)</a></code> </p>
+ </td>
+ <td><p>Confidence intervals for parameters in saem.mmkin objects</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="intervals.nlmixr.mmkin.html">intervals(<i>&lt;nlmixr.mmkin&gt;</i>)</a></code> </p>
+ </td>
+ <td><p>Confidence intervals for parameters in nlmixr.mmkin objects</p></td>
</tr>
</tbody><tbody>
<tr>
diff --git a/docs/dev/reference/intervals.nlmixr.mmkin.html b/docs/dev/reference/intervals.nlmixr.mmkin.html
new file mode 100644
index 00000000..ccc348b1
--- /dev/null
+++ b/docs/dev/reference/intervals.nlmixr.mmkin.html
@@ -0,0 +1,203 @@
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+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ <li>
+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
+ </ul>
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+
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+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Confidence intervals for parameters in nlmixr.mmkin objects</h1>
+ <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/intervals.R'><code>R/intervals.R</code></a></small>
+ <div class="hidden name"><code>intervals.nlmixr.mmkin.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Confidence intervals for parameters in nlmixr.mmkin objects</p>
+ </div>
+
+ <pre class="usage"><span class='co'># S3 method for nlmixr.mmkin</span>
+<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/intervals.html'>intervals</a></span><span class='op'>(</span><span class='va'>object</span>, level <span class='op'>=</span> <span class='fl'>0.95</span>, backtransform <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span></pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>object</th>
+ <td><p>The fitted saem.mmkin object</p></td>
+ </tr>
+ <tr>
+ <th>level</th>
+ <td><p>The confidence level.</p></td>
+ </tr>
+ <tr>
+ <th>backtransform</th>
+ <td><p>Should we backtransform the parameters where a one to
+one correlation between transformed and backtransformed parameters exists?</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>An object with 'intervals.saem.mmkin' and 'intervals.lme' in the
+class attribute</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+ <nav id="toc" data-toggle="toc" class="sticky-top">
+ <h2 data-toc-skip>Contents</h2>
+ </nav>
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+
+
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+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
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+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+</div>
+
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diff --git a/docs/dev/reference/intervals.saem.mmkin.html b/docs/dev/reference/intervals.saem.mmkin.html
new file mode 100644
index 00000000..a160b21d
--- /dev/null
+++ b/docs/dev/reference/intervals.saem.mmkin.html
@@ -0,0 +1,205 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Confidence intervals for parameters in saem.mmkin objects — intervals.saem.mmkin • mkin</title>
+
+
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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+
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+
+<!-- headroom.js -->
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+<meta property="og:title" content="Confidence intervals for parameters in saem.mmkin objects — intervals.saem.mmkin" />
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+ <a href="../reference/index.html">Functions and data</a>
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+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/mkin.html">Introduction to mkin</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ <li>
+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
+ </ul>
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+<li>
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+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Confidence intervals for parameters in saem.mmkin objects</h1>
+ <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/intervals.R'><code>R/intervals.R</code></a></small>
+ <div class="hidden name"><code>intervals.saem.mmkin.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Confidence intervals for parameters in saem.mmkin objects</p>
+ </div>
+
+ <pre class="usage"><span class='co'># S3 method for saem.mmkin</span>
+<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/intervals.html'>intervals</a></span><span class='op'>(</span><span class='va'>object</span>, level <span class='op'>=</span> <span class='fl'>0.95</span>, backtransform <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span></pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>object</th>
+ <td><p>The fitted saem.mmkin object</p></td>
+ </tr>
+ <tr>
+ <th>level</th>
+ <td><p>The confidence level. Must be the default of 0.95 as this is what
+is available in the saemix object</p></td>
+ </tr>
+ <tr>
+ <th>backtransform</th>
+ <td><p>In case the model was fitted with mkin transformations,
+should we backtransform the parameters where a one to one correlation
+between transformed and backtransformed parameters exists?</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>An object with 'intervals.saem.mmkin' and 'intervals.lme' in the
+class attribute</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+ <nav id="toc" data-toggle="toc" class="sticky-top">
+ <h2 data-toc-skip>Contents</h2>
+ </nav>
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+</div>
+
+ </footer>
+ </div>
+
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+
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+ </body>
+</html>
+
+
diff --git a/docs/dev/reference/nlmixr.mmkin.html b/docs/dev/reference/nlmixr.mmkin.html
index db114483..568078c6 100644
--- a/docs/dev/reference/nlmixr.mmkin.html
+++ b/docs/dev/reference/nlmixr.mmkin.html
@@ -210,8 +210,8 @@ Expectation Maximisation algorithm (SAEM).</p>
</tr>
<tr>
<th>error_model</th>
- <td><p>Possibility to override the error model which is being
-set based on the error model used in the mmkin row object.</p></td>
+ <td><p>Optional argument to override the error model which is
+being set based on the error model used in the mmkin row object.</p></td>
</tr>
<tr>
<th>test_log_parms</th>
@@ -290,7 +290,8 @@ obtained by fitting the same model to a list of datasets using <a href='mkinfit.
cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>f_nlmixr_sfo_saem</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"saem"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'>→ generate SAEM model</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; 1: 86.5083 -3.1968 4.1673 1.7173 48.7028
+</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'>→ generate SAEM model</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>RxODE 1.1.1 using 8 threads (see ?getRxThreads)</span>
+#&gt; <span class='message'> no cache: create with `rxCreateCache()`</span></div><div class='output co'>#&gt; 1: 86.5083 -3.1968 4.1673 1.7173 48.7028
#&gt; 2: 87.3628 -3.1468 3.9589 1.6315 45.1225
#&gt; 3: 86.8866 -3.2249 3.7610 1.8212 43.0034
#&gt; 4: 85.9210 -3.2427 3.5729 1.7302 39.4197
@@ -4502,7 +4503,7 @@ obtained by fitting the same model to a list of datasets using <a href='mkinfit.
#&gt; <span class='message'>k_A1=rx_expr_11;</span>
#&gt; <span class='message'>f_parent=1/(1+exp(-(ETA[4]+THETA[4])));</span>
#&gt; <span class='message'>tad=tad();</span>
-#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 5.579 0.328 5.909</span></div><div class='input'><span class='va'>f_nlmixr_fomc_sfo_focei_const</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_const</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"focei"</span><span class='op'>)</span>
+#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 5.546 0.379 5.924</span></div><div class='input'><span class='va'>f_nlmixr_fomc_sfo_focei_const</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_const</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"focei"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'>→ creating full model...</span></div><div class='output co'>#&gt; <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ creating full model...</span></div><div class='output co'>#&gt; <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ calculate jacobian</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate sensitivities</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate ∂(f)/∂(η)</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate ∂(R²)/∂(η)</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in inner model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in inner model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in EBE model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in EBE model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ compiling inner model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in FD model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in FD model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ compiling EBE model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ compiling events FD model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>Model:</span></div><div class='output co'>#&gt; <span class='message'>cmt(parent);</span>
#&gt; <span class='message'>cmt(A1);</span>
#&gt; <span class='message'>rx_expr_6~ETA[1]+THETA[1];</span>
@@ -4551,7 +4552,7 @@ obtained by fitting the same model to a list of datasets using <a href='mkinfit.
#&gt; <span class='message'>beta=exp(rx_expr_8);</span>
#&gt; <span class='message'>f_parent=1/(1+exp(-(ETA[3]+THETA[3])));</span>
#&gt; <span class='message'>tad=tad();</span>
-#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 7.125 0.34 7.462</span></div><div class='input'><span class='va'>f_nlmixr_dfop_sfo_focei_const</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_const</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"focei"</span><span class='op'>)</span>
+#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 6.842 0.338 7.177</span></div><div class='input'><span class='va'>f_nlmixr_dfop_sfo_focei_const</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_const</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"focei"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'>→ creating full model...</span></div><div class='output co'>#&gt; <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ creating full model...</span></div><div class='output co'>#&gt; <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ calculate jacobian</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate sensitivities</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate ∂(f)/∂(η)</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate ∂(R²)/∂(η)</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in inner model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in inner model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in EBE model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in EBE model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ compiling inner model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in FD model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in FD model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ compiling EBE model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ compiling events FD model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>Model:</span></div><div class='output co'>#&gt; <span class='message'>cmt(parent);</span>
#&gt; <span class='message'>cmt(A1);</span>
#&gt; <span class='message'>rx_expr_6~ETA[1]+THETA[1];</span>
@@ -4608,10 +4609,10 @@ obtained by fitting the same model to a list of datasets using <a href='mkinfit.
#&gt; <span class='message'>f_parent=1/(1+exp(-(ETA[3]+THETA[3])));</span>
#&gt; <span class='message'>g=1/(rx_expr_20);</span>
#&gt; <span class='message'>tad=tad();</span>
-#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 15.03 0.407 15.43</span></div><div class='input'>
+#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 15.14 0.971 16.13</span></div><div class='input'>
<span class='co'># Variance by variable is supported by 'saem' and 'focei'</span>
<span class='va'>f_nlmixr_fomc_sfo_saem_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_obs</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"saem"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'>→ generate SAEM model</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='error'>Error in configsaem(model = model, data = dat, inits = inits, mcmc = .mcmc, ODEopt = .ODEopt, seed = .seed, distribution = .dist, DEBUG = .DEBUG, addProp = .addProp, tol = .tol, itmax = .itmax, type = .type, powRange = .powRange, lambdaRange = .lambdaRange): covariate(s) not found: f_parent_to_A1</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 1.253 0.121 1.373</span></div><div class='input'><span class='va'>f_nlmixr_fomc_sfo_focei_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_obs</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"focei"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'>→ generate SAEM model</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='error'>Error in configsaem(model = model, data = dat, inits = inits, mcmc = .mcmc, ODEopt = .ODEopt, seed = .seed, distribution = .dist, DEBUG = .DEBUG, addProp = .addProp, tol = .tol, itmax = .itmax, type = .type, powRange = .powRange, lambdaRange = .lambdaRange): covariate(s) not found: f_parent_to_A1</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 1.271 0.123 1.393</span></div><div class='input'><span class='va'>f_nlmixr_fomc_sfo_focei_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_obs</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"focei"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'>→ creating full model...</span></div><div class='output co'>#&gt; <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ creating full model...</span></div><div class='output co'>#&gt; <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ calculate jacobian</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate sensitivities</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate ∂(f)/∂(η)</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate ∂(R²)/∂(η)</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in inner model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in inner model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in EBE model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in EBE model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ compiling inner model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in FD model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in FD model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ compiling EBE model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ compiling events FD model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>Model:</span></div><div class='output co'>#&gt; <span class='message'>cmt(parent);</span>
#&gt; <span class='message'>cmt(A1);</span>
#&gt; <span class='message'>rx_expr_6~ETA[1]+THETA[1];</span>
@@ -4660,8 +4661,8 @@ obtained by fitting the same model to a list of datasets using <a href='mkinfit.
#&gt; <span class='message'>beta=exp(rx_expr_8);</span>
#&gt; <span class='message'>f_parent=1/(1+exp(-(ETA[3]+THETA[3])));</span>
#&gt; <span class='message'>tad=tad();</span>
-#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 6.487 0.387 6.872</span></div><div class='input'><span class='va'>f_nlmixr_dfop_sfo_saem_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_obs</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"saem"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'>→ generate SAEM model</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='error'>Error in configsaem(model = model, data = dat, inits = inits, mcmc = .mcmc, ODEopt = .ODEopt, seed = .seed, distribution = .dist, DEBUG = .DEBUG, addProp = .addProp, tol = .tol, itmax = .itmax, type = .type, powRange = .powRange, lambdaRange = .lambdaRange): covariate(s) not found: f_parent_to_A1</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 1.385 0.1 1.485</span></div><div class='input'><span class='va'>f_nlmixr_dfop_sfo_focei_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_obs</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"focei"</span><span class='op'>)</span>
+#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 6.699 0.341 7.038</span></div><div class='input'><span class='va'>f_nlmixr_dfop_sfo_saem_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_obs</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"saem"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'>→ generate SAEM model</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='error'>Error in configsaem(model = model, data = dat, inits = inits, mcmc = .mcmc, ODEopt = .ODEopt, seed = .seed, distribution = .dist, DEBUG = .DEBUG, addProp = .addProp, tol = .tol, itmax = .itmax, type = .type, powRange = .powRange, lambdaRange = .lambdaRange): covariate(s) not found: f_parent_to_A1</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 1.384 0.092 1.477</span></div><div class='input'><span class='va'>f_nlmixr_dfop_sfo_focei_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_obs</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"focei"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'>→ creating full model...</span></div><div class='output co'>#&gt; <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ creating full model...</span></div><div class='output co'>#&gt; <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ calculate jacobian</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate sensitivities</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate ∂(f)/∂(η)</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate ∂(R²)/∂(η)</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in inner model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in inner model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in EBE model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in EBE model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ compiling inner model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in FD model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in FD model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ compiling EBE model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ compiling events FD model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>Model:</span></div><div class='output co'>#&gt; <span class='message'>cmt(parent);</span>
#&gt; <span class='message'>cmt(A1);</span>
#&gt; <span class='message'>rx_expr_6~ETA[1]+THETA[1];</span>
@@ -4718,7 +4719,7 @@ obtained by fitting the same model to a list of datasets using <a href='mkinfit.
#&gt; <span class='message'>f_parent=1/(1+exp(-(ETA[3]+THETA[3])));</span>
#&gt; <span class='message'>g=1/(rx_expr_19);</span>
#&gt; <span class='message'>tad=tad();</span>
-#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 15.06 0.434 15.49</span></div><div class='input'>
+#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 14.86 1.172 16.03</span></div><div class='input'>
<span class='co'># Identical two-component error for all variables is only possible with</span>
<span class='co'># est = 'focei' in nlmixr</span>
<span class='va'>f_nlmixr_fomc_sfo_focei_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_tc</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"focei"</span><span class='op'>)</span>
@@ -4772,7 +4773,7 @@ obtained by fitting the same model to a list of datasets using <a href='mkinfit.
#&gt; <span class='message'>beta=exp(rx_expr_8);</span>
#&gt; <span class='message'>f_parent=1/(1+exp(-(ETA[3]+THETA[3])));</span>
#&gt; <span class='message'>tad=tad();</span>
-#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 8.599 0.38 8.975</span></div><div class='input'><span class='va'>f_nlmixr_dfop_sfo_focei_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_tc</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"focei"</span><span class='op'>)</span>
+#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 8.461 0.404 8.863</span></div><div class='input'><span class='va'>f_nlmixr_dfop_sfo_focei_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_tc</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"focei"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'>→ creating full model...</span></div><div class='output co'>#&gt; <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ creating full model...</span></div><div class='output co'>#&gt; <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ calculate jacobian</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate sensitivities</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate ∂(f)/∂(η)</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate ∂(R²)/∂(η)</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in inner model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in inner model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in EBE model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in EBE model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ compiling inner model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in FD model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in FD model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ compiling EBE model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ compiling events FD model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>Model:</span></div><div class='output co'>#&gt; <span class='message'>cmt(parent);</span>
#&gt; <span class='message'>cmt(A1);</span>
#&gt; <span class='message'>rx_expr_6~ETA[1]+THETA[1];</span>
@@ -4831,12 +4832,12 @@ obtained by fitting the same model to a list of datasets using <a href='mkinfit.
#&gt; <span class='message'>f_parent=1/(1+exp(-(ETA[3]+THETA[3])));</span>
#&gt; <span class='message'>g=1/(rx_expr_21);</span>
#&gt; <span class='message'>tad=tad();</span>
-#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 17.64 0.453 18.09</span></div><div class='input'>
+#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 18.02 0.925 18.94</span></div><div class='input'>
<span class='co'># Two-component error by variable is possible with both estimation methods</span>
<span class='co'># Variance by variable is supported by 'saem' and 'focei'</span>
<span class='va'>f_nlmixr_fomc_sfo_saem_obs_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_tc</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"saem"</span>,
error_model <span class='op'>=</span> <span class='st'>"obs_tc"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='error'>Error in configsaem(model = model, data = dat, inits = inits, mcmc = .mcmc, ODEopt = .ODEopt, seed = .seed, distribution = .dist, DEBUG = .DEBUG, addProp = .addProp, tol = .tol, itmax = .itmax, type = .type, powRange = .powRange, lambdaRange = .lambdaRange): covariate(s) not found: f_parent_to_A1</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.772 0.04 0.813</span></div><div class='input'><span class='va'>f_nlmixr_fomc_sfo_focei_obs_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_tc</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"focei"</span>,
+</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='error'>Error in configsaem(model = model, data = dat, inits = inits, mcmc = .mcmc, ODEopt = .ODEopt, seed = .seed, distribution = .dist, DEBUG = .DEBUG, addProp = .addProp, tol = .tol, itmax = .itmax, type = .type, powRange = .powRange, lambdaRange = .lambdaRange): covariate(s) not found: f_parent_to_A1</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.782 0.02 0.803</span></div><div class='input'><span class='va'>f_nlmixr_fomc_sfo_focei_obs_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_tc</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"focei"</span>,
error_model <span class='op'>=</span> <span class='st'>"obs_tc"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'>→ creating full model...</span></div><div class='output co'>#&gt; <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ creating full model...</span></div><div class='output co'>#&gt; <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ calculate jacobian</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate sensitivities</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate ∂(f)/∂(η)</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate ∂(R²)/∂(η)</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in inner model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in inner model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in EBE model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in EBE model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ compiling inner model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in FD model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in FD model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ compiling EBE model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ compiling events FD model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>Model:</span></div><div class='output co'>#&gt; <span class='message'>cmt(parent);</span>
#&gt; <span class='message'>cmt(A1);</span>
@@ -4888,9 +4889,9 @@ obtained by fitting the same model to a list of datasets using <a href='mkinfit.
#&gt; <span class='message'>beta=exp(rx_expr_8);</span>
#&gt; <span class='message'>f_parent=1/(1+exp(-(ETA[3]+THETA[3])));</span>
#&gt; <span class='message'>tad=tad();</span>
-#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 8.33 0.419 8.745</span></div><div class='input'><span class='va'>f_nlmixr_dfop_sfo_saem_obs_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_tc</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"saem"</span>,
+#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 8.173 0.405 8.575</span></div><div class='input'><span class='va'>f_nlmixr_dfop_sfo_saem_obs_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_tc</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"saem"</span>,
error_model <span class='op'>=</span> <span class='st'>"obs_tc"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='error'>Error in configsaem(model = model, data = dat, inits = inits, mcmc = .mcmc, ODEopt = .ODEopt, seed = .seed, distribution = .dist, DEBUG = .DEBUG, addProp = .addProp, tol = .tol, itmax = .itmax, type = .type, powRange = .powRange, lambdaRange = .lambdaRange): covariate(s) not found: f_parent_to_A1</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.832 0.032 0.866</span></div><div class='input'><span class='va'>f_nlmixr_dfop_sfo_focei_obs_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_tc</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"focei"</span>,
+</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='error'>Error in configsaem(model = model, data = dat, inits = inits, mcmc = .mcmc, ODEopt = .ODEopt, seed = .seed, distribution = .dist, DEBUG = .DEBUG, addProp = .addProp, tol = .tol, itmax = .itmax, type = .type, powRange = .powRange, lambdaRange = .lambdaRange): covariate(s) not found: f_parent_to_A1</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.824 0.024 0.851</span></div><div class='input'><span class='va'>f_nlmixr_dfop_sfo_focei_obs_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></span><span class='op'>(</span><span class='va'>f_mmkin_tc</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>, est <span class='op'>=</span> <span class='st'>"focei"</span>,
error_model <span class='op'>=</span> <span class='st'>"obs_tc"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> parameter labels from comments are typically ignored in non-interactive mode</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BBBB;'>ℹ</span> Need to run with the source intact to parse comments</span></div><div class='output co'>#&gt; <span class='message'>→ creating full model...</span></div><div class='output co'>#&gt; <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ creating full model...</span></div><div class='output co'>#&gt; <span class='message'>→ pruning branches (<span style='color: #262626; background-color: #DADADA;'>`if`</span>/<span style='color: #262626; background-color: #DADADA;'>`else`</span>)...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ loading into <span style='color: #0000BB;'>symengine</span> environment...</span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ calculate jacobian</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate sensitivities</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate ∂(f)/∂(η)</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ calculate ∂(R²)/∂(η)</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in inner model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in inner model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in EBE model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in EBE model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ compiling inner model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ finding duplicate expressions in FD model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ optimizing duplicate expressions in FD model...</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'>→ compiling EBE model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>→ compiling events FD model...</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>✔</span> done</span></div><div class='output co'>#&gt; <span class='message'>Model:</span></div><div class='output co'>#&gt; <span class='message'>cmt(parent);</span>
#&gt; <span class='message'>cmt(A1);</span>
@@ -4950,7 +4951,7 @@ obtained by fitting the same model to a list of datasets using <a href='mkinfit.
#&gt; <span class='message'>f_parent=1/(1+exp(-(ETA[3]+THETA[3])));</span>
#&gt; <span class='message'>g=1/(rx_expr_19);</span>
#&gt; <span class='message'>tad=tad();</span>
-#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 18.15 0.42 18.57</span></div><div class='input'>
+#&gt; <span class='message'>dosenum=dosenum();</span></div><div class='output co'>#&gt; <span class='message'>Needed Covariates:</span></div><div class='output co'>#&gt; <span class='message'>[1] "f_parent_to_A1" "CMT" </span></div><div class='output co'>#&gt; <span class='error'>Error in (function (data, inits, PKpars, model = NULL, pred = NULL, err = NULL, lower = -Inf, upper = Inf, fixed = NULL, skipCov = NULL, control = foceiControl(), thetaNames = NULL, etaNames = NULL, etaMat = NULL, ..., env = NULL, keep = NULL, drop = NULL) { set.seed(control$seed) .pt &lt;- proc.time() RxODE::.setWarnIdSort(FALSE) on.exit(RxODE::.setWarnIdSort(TRUE)) loadNamespace("n1qn1") if (!RxODE::rxIs(control, "foceiControl")) { control &lt;- do.call(foceiControl, control) } if (is.null(env)) { .ret &lt;- new.env(parent = emptyenv()) } else { .ret &lt;- env } .ret$origData &lt;- data .ret$etaNames &lt;- etaNames .ret$thetaFixed &lt;- fixed .ret$control &lt;- control .ret$control$focei.mu.ref &lt;- integer(0) if (is(model, "RxODE") || is(model, "character")) { .ret$ODEmodel &lt;- TRUE if (class(pred) != "function") { stop("pred must be a function specifying the prediction variables in this model.") } } else { .ret$ODEmodel &lt;- TRUE model &lt;- RxODE::rxGetLin(PKpars) pred &lt;- eval(parse(text = "function(){return(Central);}")) } .square &lt;- function(x) x * x .ret$diagXformInv &lt;- c(sqrt = ".square", log = "exp", identity = "identity")[control$diagXform] if (is.null(err)) { err &lt;- eval(parse(text = paste0("function(){err", paste(inits$ERROR[[1]], collapse = ""), "}"))) } .covNames &lt;- .parNames &lt;- c() .ret$adjLik &lt;- control$adjLik .mixed &lt;- !is.null(inits$OMGA) &amp;&amp; length(inits$OMGA) &gt; 0 if (!exists("noLik", envir = .ret)) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ssAtol &lt;- rep(control$ssAtol, length(RxODE::rxModelVars(model)$state)) .ssRtol &lt;- rep(control$ssRtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = (control$derivMethod == 2L), pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, interaction = (control$interaction == 1L), only.numeric = !.mixed, run.internal = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol .ssAtol &lt;- c(.ssAtol, rep(control$ssAtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssAtol))) .ssRtol &lt;- c(.ssRtol, rep(control$ssRtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.ssRtol))) .ret$control$rxControl$ssAtol &lt;- .ssAtol .ret$control$rxControl$ssRtol &lt;- .ssRtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { if (.ret$noLik) { .atol &lt;- rep(control$atol, length(RxODE::rxModelVars(model)$state)) .rtol &lt;- rep(control$rtol, length(RxODE::rxModelVars(model)$state)) .ret$model &lt;- RxODE::rxSymPySetupPred(model, pred, PKpars, err, grad = FALSE, pred.minus.dv = TRUE, sum.prod = control$sumProd, theta.derivs = FALSE, optExpression = control$optExpression, run.internal = TRUE, only.numeric = TRUE, addProp = control$addProp) if (!is.null(.ret$model$inner)) { .atol &lt;- c(.atol, rep(control$atolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.atol))) .rtol &lt;- c(.rtol, rep(control$rtolSens, length(RxODE::rxModelVars(.ret$model$inner)$state) - length(.rtol))) .ret$control$rxControl$atol &lt;- .atol .ret$control$rxControl$rtol &lt;- .rtol } .covNames &lt;- .parNames &lt;- RxODE::rxParams(.ret$model$pred.only) .covNames &lt;- .covNames[regexpr(rex::rex(start, or("THETA", "ETA"), "[", numbers, "]", end), .covNames) == -1] colnames(data) &lt;- sapply(names(data), function(x) { if (any(x == .covNames)) { return(x) } else { return(toupper(x)) } }) .lhs &lt;- c(names(RxODE::rxInits(.ret$model$pred.only)), RxODE::rxLhs(.ret$model$pred.only)) if (length(.lhs) &gt; 0) { .covNames &lt;- .covNames[regexpr(rex::rex(start, or(.lhs), end), .covNames) == -1] } if (length(.covNames) &gt; 0) { if (!all(.covNames %in% names(data))) { message("Model:") RxODE::rxCat(.ret$model$pred.only) message("Needed Covariates:") nlmixrPrint(.covNames) stop("Not all the covariates are in the dataset.") } message("Needed Covariates:") print(.covNames) } .extraPars &lt;- .ret$model$extra.pars } else { .extraPars &lt;- NULL } } .ret$skipCov &lt;- skipCov if (is.null(skipCov)) { if (is.null(fixed)) { .tmp &lt;- rep(FALSE, length(inits$THTA)) } else { if (length(fixed) &lt; length(inits$THTA)) { .tmp &lt;- c(fixed, rep(FALSE, length(inits$THTA) - length(fixed))) } else { .tmp &lt;- fixed[1:length(inits$THTA)] } } if (exists("uif", envir = .ret)) { .uifErr &lt;- .ret$uif$ini$err[!is.na(.ret$uif$ini$ntheta)] .uifErr &lt;- sapply(.uifErr, function(x) { if (is.na(x)) { return(FALSE) } return(!any(x == c("pow2", "tbs", "tbsYj"))) }) .tmp &lt;- (.tmp | .uifErr) } .ret$skipCov &lt;- c(.tmp, rep(TRUE, length(.extraPars))) .ret$control$focei.mu.ref &lt;- .ret$uif$focei.mu.ref } if (is.null(.extraPars)) { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA))) } else { .nms &lt;- c(sprintf("THETA[%s]", seq_along(inits$THTA)), sprintf("ERR[%s]", seq_along(.extraPars))) } if (!is.null(thetaNames) &amp;&amp; (length(inits$THTA) + length(.extraPars)) == length(thetaNames)) { .nms &lt;- thetaNames } .ret$thetaNames &lt;- .nms .thetaReset$thetaNames &lt;- .nms if (length(lower) == 1) { lower &lt;- rep(lower, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { print(inits$THTA) print(lower) stop("Lower must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (length(upper) == 1) { upper &lt;- rep(upper, length(inits$THTA)) } else if (length(lower) != length(inits$THTA)) { stop("Upper must be a single constant for all the THETA lower bounds, or match the dimension of THETA.") } if (!is.null(.extraPars)) { .ret$model$extra.pars &lt;- eval(call(control$diagXform, .ret$model$extra.pars)) if (length(.ret$model$extra.pars) &gt; 0) { inits$THTA &lt;- c(inits$THTA, .ret$model$extra.pars) .lowerErr &lt;- rep(control$atol[1] * 10, length(.ret$model$extra.pars)) .upperErr &lt;- rep(Inf, length(.ret$model$extra.pars)) lower &lt;- c(lower, .lowerErr) upper &lt;- c(upper, .upperErr) } } if (is.null(data$ID)) stop("\"ID\" not found in data") if (is.null(data$DV)) stop("\"DV\" not found in data") if (is.null(data$EVID)) data$EVID &lt;- 0 if (is.null(data$AMT)) data$AMT &lt;- 0 for (.v in c("TIME", "AMT", "DV", .covNames)) { data[[.v]] &lt;- as.double(data[[.v]]) } .ret$dataSav &lt;- data .ds &lt;- data[data$EVID != 0 &amp; data$EVID != 2, c("ID", "TIME", "AMT", "EVID", .covNames)] .w &lt;- which(tolower(names(data)) == "limit") .limitName &lt;- NULL if (length(.w) == 1L) { .limitName &lt;- names(data)[.w] } .censName &lt;- NULL .w &lt;- which(tolower(names(data)) == "cens") if (length(.w) == 1L) { .censName &lt;- names(data[.w]) } data &lt;- data[data$EVID == 0 | data$EVID == 2, c("ID", "TIME", "DV", "EVID", .covNames, .limitName, .censName)] .w &lt;- which(!(names(.ret$dataSav) %in% c(.covNames, keep))) names(.ret$dataSav)[.w] &lt;- tolower(names(.ret$dataSav[.w])) if (.mixed) { .lh &lt;- .parseOM(inits$OMGA) .nlh &lt;- sapply(.lh, length) .osplt &lt;- rep(1:length(.lh), .nlh) .lini &lt;- list(inits$THTA, unlist(.lh)) .nlini &lt;- sapply(.lini, length) .nsplt &lt;- rep(1:length(.lini), .nlini) .om0 &lt;- .genOM(.lh) if (length(etaNames) == dim(.om0)[1]) { .ret$etaNames &lt;- .ret$etaNames } else { .ret$etaNames &lt;- sprintf("ETA[%d]", seq(1, dim(.om0)[1])) } .ret$rxInv &lt;- RxODE::rxSymInvCholCreate(mat = .om0, diag.xform = control$diagXform) .ret$xType &lt;- .ret$rxInv$xType .om0a &lt;- .om0 .om0a &lt;- .om0a/control$diagOmegaBoundLower .om0b &lt;- .om0 .om0b &lt;- .om0b * control$diagOmegaBoundUpper .om0a &lt;- RxODE::rxSymInvCholCreate(mat = .om0a, diag.xform = control$diagXform) .om0b &lt;- RxODE::rxSymInvCholCreate(mat = .om0b, diag.xform = control$diagXform) .omdf &lt;- data.frame(a = .om0a$theta, m = .ret$rxInv$theta, b = .om0b$theta, diag = .om0a$theta.diag) .omdf$lower &lt;- with(.omdf, ifelse(a &gt; b, b, a)) .omdf$lower &lt;- with(.omdf, ifelse(lower == m, -Inf, lower)) .omdf$lower &lt;- with(.omdf, ifelse(!diag, -Inf, lower)) .omdf$upper &lt;- with(.omdf, ifelse(a &lt; b, b, a)) .omdf$upper &lt;- with(.omdf, ifelse(upper == m, Inf, upper)) .omdf$upper &lt;- with(.omdf, ifelse(!diag, Inf, upper)) .ret$control$nomega &lt;- length(.omdf$lower) .ret$control$neta &lt;- sum(.omdf$diag) .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) lower &lt;- c(lower, .omdf$lower) upper &lt;- c(upper, .omdf$upper) } else { .ret$control$nomega &lt;- 0 .ret$control$neta &lt;- 0 .ret$xType &lt;- -1 .ret$control$ntheta &lt;- length(lower) .ret$control$nfixed &lt;- sum(fixed) } .ret$lower &lt;- lower .ret$upper &lt;- upper .ret$thetaIni &lt;- inits$THTA .scaleC &lt;- double(length(lower)) if (is.null(control$scaleC)) { .scaleC &lt;- rep(NA_real_, length(lower)) } else { .scaleC &lt;- as.double(control$scaleC) if (length(lower) &gt; length(.scaleC)) { .scaleC &lt;- c(.scaleC, rep(NA_real_, length(lower) - length(.scaleC))) } else if (length(lower) &lt; length(.scaleC)) { .scaleC &lt;- .scaleC[seq(1, length(lower))] warning("scaleC control option has more options than estimated population parameters, please check.") } } .ret$scaleC &lt;- .scaleC if (exists("uif", envir = .ret)) { .ini &lt;- as.data.frame(.ret$uif$ini)[!is.na(.ret$uif$ini$err), c("est", "err", "ntheta")] for (.i in seq_along(.ini$err)) { if (is.na(.ret$scaleC[.ini$ntheta[.i]])) { if (any(.ini$err[.i] == c("boxCox", "yeoJohnson", "pow2", "tbs", "tbsYj"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 1 } else if (any(.ini$err[.i] == c("prop", "add", "norm", "dnorm", "logn", "dlogn", "lnorm", "dlnorm"))) { .ret$scaleC[.ini$ntheta[.i]] &lt;- 0.5 * abs(.ini$est[.i]) } } } for (.i in .ini$model$extraProps$powTheta) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- 1 } .ini &lt;- as.data.frame(.ret$uif$ini) for (.i in .ini$model$extraProps$factorial) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i] + 1)) } for (.i in .ini$model$extraProps$gamma) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- abs(1/digamma(.ini$est[.i])) } for (.i in .ini$model$extraProps$log) { if (is.na(.ret$scaleC[.i])) .ret$scaleC[.i] &lt;- log(abs(.ini$est[.i])) * abs(.ini$est[.i]) } for (.i in .ret$logitThetas) { .b &lt;- .ret$logitThetasLow[.i] .c &lt;- .ret$logitThetasHi[.i] .a &lt;- .ini$est[.i] if (is.na(.ret$scaleC[.i])) { .ret$scaleC[.i] &lt;- 1 * (-.b + .c) * exp(-.a)/((1 + exp(-.a))^2 * (.b + 1 * (-.b + .c)/(1 + exp(-.a)))) } } } names(.ret$thetaIni) &lt;- sprintf("THETA[%d]", seq_along(.ret$thetaIni)) if (is.null(etaMat) &amp; !is.null(control$etaMat)) { .ret$etaMat &lt;- control$etaMat } else { .ret$etaMat &lt;- etaMat } .ret$setupTime &lt;- (proc.time() - .pt)["elapsed"] if (exists("uif", envir = .ret)) { .tmp &lt;- .ret$uif$logThetasList .ret$logThetas &lt;- .tmp[[1]] .ret$logThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasList .ret$logitThetas &lt;- .tmp[[1]] .ret$logitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListLow .ret$logitThetasLow &lt;- .tmp[[1]] .ret$logitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$logitThetasListHi .ret$logitThetasHi &lt;- .tmp[[1]] .ret$logitThetasHiF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasList .ret$probitThetas &lt;- .tmp[[1]] .ret$probitThetasF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListLow .ret$probitThetasLow &lt;- .tmp[[1]] .ret$probitThetasLowF &lt;- .tmp[[2]] .tmp &lt;- .ret$uif$probitThetasListHi .ret$probitThetasHi &lt;- .tmp[[1]] .ret$probitThetasHiF &lt;- .tmp[[2]] } else { .ret$logThetasF &lt;- integer(0) .ret$logitThetasF &lt;- integer(0) .ret$logitThetasHiF &lt;- numeric(0) .ret$logitThetasLowF &lt;- numeric(0) .ret$logitThetas &lt;- integer(0) .ret$logitThetasHi &lt;- numeric(0) .ret$logitThetasLow &lt;- numeric(0) .ret$probitThetasF &lt;- integer(0) .ret$probitThetasHiF &lt;- numeric(0) .ret$probitThetasLowF &lt;- numeric(0) .ret$probitThetas &lt;- integer(0) .ret$probitThetasHi &lt;- numeric(0) .ret$probitThetasLow &lt;- numeric(0) } if (exists("noLik", envir = .ret)) { if (!.ret$noLik) { .ret$.params &lt;- c(sprintf("THETA[%d]", seq_along(.ret$thetaIni)), sprintf("ETA[%d]", seq(1, dim(.om0)[1]))) .ret$.thetan &lt;- length(.ret$thetaIni) .ret$nobs &lt;- sum(data$EVID == 0) } } .ret$control$printTop &lt;- TRUE .ret$control$nF &lt;- 0 .est0 &lt;- .ret$thetaIni if (!is.null(.ret$model$pred.nolhs)) { .ret$control$predNeq &lt;- length(.ret$model$pred.nolhs$state) } else { .ret$control$predNeq &lt;- 0L } .fitFun &lt;- function(.ret) { this.env &lt;- environment() assign("err", "theta reset", this.env) while (this.env$err == "theta reset") { assign("err", "", this.env) .ret0 &lt;- tryCatch({ foceiFitCpp_(.ret) }, error = function(e) { if (regexpr("theta reset", e$message) != -1) { assign("zeroOuter", FALSE, this.env) assign("zeroGrad", FALSE, this.env) if (regexpr("theta reset0", e$message) != -1) { assign("zeroGrad", TRUE, this.env) } else if (regexpr("theta resetZ", e$message) != -1) { assign("zeroOuter", TRUE, this.env) } assign("err", "theta reset", this.env) } else { assign("err", e$message, this.env) } }) if (this.env$err == "theta reset") { .nm &lt;- names(.ret$thetaIni) .ret$thetaIni &lt;- setNames(.thetaReset$thetaIni + 0, .nm) .ret$rxInv$theta &lt;- .thetaReset$omegaTheta .ret$control$printTop &lt;- FALSE .ret$etaMat &lt;- .thetaReset$etaMat .ret$control$etaMat &lt;- .thetaReset$etaMat .ret$control$maxInnerIterations &lt;- .thetaReset$maxInnerIterations .ret$control$nF &lt;- .thetaReset$nF .ret$control$gillRetC &lt;- .thetaReset$gillRetC .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillRet &lt;- .thetaReset$gillRet .ret$control$gillDf &lt;- .thetaReset$gillDf .ret$control$gillDf2 &lt;- .thetaReset$gillDf2 .ret$control$gillErr &lt;- .thetaReset$gillErr .ret$control$rEps &lt;- .thetaReset$rEps .ret$control$aEps &lt;- .thetaReset$aEps .ret$control$rEpsC &lt;- .thetaReset$rEpsC .ret$control$aEpsC &lt;- .thetaReset$aEpsC .ret$control$c1 &lt;- .thetaReset$c1 .ret$control$c2 &lt;- .thetaReset$c2 if (this.env$zeroOuter) { message("Posthoc reset") .ret$control$maxOuterIterations &lt;- 0L } else if (this.env$zeroGrad) { message("Theta reset (zero gradient values); Switch to bobyqa") RxODE::rxReq("minqa") .ret$control$outerOptFun &lt;- .bobyqa .ret$control$outerOpt &lt;- -1L } else { message("Theta reset (ETA drift)") } } } if (this.env$err != "") { stop(this.env$err) } else { return(.ret0) } } .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- 1 while (inherits(.ret0, "try-error") &amp;&amp; control$maxOuterIterations != 0 &amp;&amp; .n &lt;= control$nRetries) { message(sprintf("Restart %s", .n)) .ret$control$nF &lt;- 0 .estNew &lt;- .est0 + 0.2 * .n * abs(.est0) * stats::runif(length(.est0)) - 0.1 * .n .estNew &lt;- sapply(seq_along(.est0), function(.i) { if (.ret$thetaFixed[.i]) { return(.est0[.i]) } else if (.estNew[.i] &lt; lower[.i]) { return(lower + (.Machine$double.eps)^(1/7)) } else if (.estNew[.i] &gt; upper[.i]) { return(upper - (.Machine$double.eps)^(1/7)) } else { return(.estNew[.i]) } }) .ret$thetaIni &lt;- .estNew .ret0 &lt;- try(.fitFun(.ret)) .n &lt;- .n + 1 } if (inherits(.ret0, "try-error")) stop("Could not fit data.") .ret &lt;- .ret0 if (exists("parHistData", .ret)) { .tmp &lt;- .ret$parHistData .tmp &lt;- .tmp[.tmp$type == "Unscaled", names(.tmp) != "type"] .iter &lt;- .tmp$iter .tmp &lt;- .tmp[, names(.tmp) != "iter"] .ret$parHistStacked &lt;- data.frame(stack(.tmp), iter = .iter) names(.ret$parHistStacked) &lt;- c("val", "par", "iter") .ret$parHist &lt;- data.frame(iter = .iter, .tmp) } if (.mixed) { .etas &lt;- .ret$ranef .thetas &lt;- .ret$fixef .pars &lt;- .Call(`_nlmixr_nlmixrParameters`, .thetas, .etas) .ret$shrink &lt;- .Call(`_nlmixr_calcShrinkOnly`, .ret$omega, .pars$eta.lst, length(.etas$ID)) .updateParFixed(.ret) } else { .updateParFixed(.ret) } if (!exists("table", .ret)) { .ret$table &lt;- tableControl() } if (control$calcTables) { .ret &lt;- addTable(.ret, updateObject = "no", keep = keep, drop = drop, table = .ret$table) } .ret})(data = dat, inits = .FoceiInits, PKpars = .pars, model = .mod, pred = function() { return(nlmixr_pred) }, err = uif$error, lower = uif$focei.lower, upper = uif$focei.upper, fixed = uif$focei.fixed, thetaNames = uif$focei.names, etaNames = uif$eta.names, control = control, env = env, keep = .keep, drop = .drop): Not all the covariates are in the dataset.</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 17.44 0.876 18.31</span></div><div class='input'>
<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span>
<span class='va'>f_nlmixr_sfo_sfo_focei_const</span><span class='op'>$</span><span class='va'>nm</span>,
<span class='va'>f_nlmixr_fomc_sfo_focei_const</span><span class='op'>$</span><span class='va'>nm</span>,
diff --git a/docs/dev/reference/reexports.html b/docs/dev/reference/reexports.html
index ac4fa4d9..4fe5164b 100644
--- a/docs/dev/reference/reexports.html
+++ b/docs/dev/reference/reexports.html
@@ -45,7 +45,7 @@ below to see their documentation.
lmtestlrtest
- nlmenlme
+ nlmeintervals, nlme
nlmixrnlmixr
@@ -148,7 +148,7 @@ below to see their documentation.
<div class="col-md-9 contents">
<div class="page-header">
<h1>Objects exported from other packages</h1>
- <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/lrtest.mkinfit.R'><code>R/lrtest.mkinfit.R</code></a>, <a href='https://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a>, <a href='https://github.com/jranke/mkin/blob/master/R/nlmixr.R'><code>R/nlmixr.R</code></a></small>
+ <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/intervals.R'><code>R/intervals.R</code></a>, <a href='https://github.com/jranke/mkin/blob/master/R/lrtest.mkinfit.R'><code>R/lrtest.mkinfit.R</code></a>, <a href='https://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a>, and 1 more</small>
<div class="hidden name"><code>reexports.Rd</code></div>
</div>
@@ -158,7 +158,7 @@ below to see their documentation.</p>
<dl>
<dt>lmtest</dt><dd><p><code><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></code></p></dd>
- <dt>nlme</dt><dd><p><code><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></code></p></dd>
+ <dt>nlme</dt><dd><p><code><a href='https://rdrr.io/pkg/nlme/man/intervals.html'>intervals</a></code>, <code><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></code></p></dd>
<dt>nlmixr</dt><dd><p><code><a href='https://rdrr.io/pkg/nlmixr/man/nlmixr.html'>nlmixr</a></code></p></dd>

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