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-rw-r--r--NAMESPACE1
-rw-r--r--R/nlme.mmkin.R7
-rw-r--r--R/saemix.R30
-rw-r--r--R/summary.nlme.mmkin.R14
-rw-r--r--R/summary.saem.mmkin.R16
-rw-r--r--docs/dev/news/index.html3
-rw-r--r--docs/dev/pkgdown.yml2
-rw-r--r--docs/dev/reference/index.html2
-rw-r--r--docs/dev/reference/nlme.mmkin.html35
-rw-r--r--docs/dev/reference/saem.html95
-rw-r--r--man/nlme.mmkin.Rd7
-rw-r--r--man/saem.Rd7
12 files changed, 137 insertions, 82 deletions
diff --git a/NAMESPACE b/NAMESPACE
index a7aa9eeb..e85f8311 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -25,6 +25,7 @@ S3method(print,mkinmod)
S3method(print,mmkin)
S3method(print,nafta)
S3method(print,nlme.mmkin)
+S3method(print,saem.mmkin)
S3method(print,summary.mkinfit)
S3method(print,summary.nlme.mmkin)
S3method(print,summary.saem.mmkin)
diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R
index d26b86ac..a9e1694f 100644
--- a/R/nlme.mmkin.R
+++ b/R/nlme.mmkin.R
@@ -210,7 +210,8 @@ nlme.mmkin <- function(model, data = sys.frame(sys.parent()),
#' @export
#' @rdname nlme.mmkin
#' @param x An nlme.mmkin object to print
-print.nlme.mmkin <- function(x, ...) {
+#' @param digits Number of digits to use for printing
+print.nlme.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...) {
cat( "Kinetic nonlinear mixed-effects model fit by " )
cat( if(x$method == "REML") "REML\n" else "maximum likelihood\n")
cat("\nStructural model:\n")
@@ -230,9 +231,9 @@ print.nlme.mmkin <- function(x, ...) {
x$call$fixed
else
lapply(fixF, function(el) as.name(deparse(el)))), "\n")
- print(fixef(x), ...)
+ print(fixef(x), digits = digits, ...)
cat("\n")
- print(summary(x$modelStruct), sigma = x$sigma, ...)
+ print(summary(x$modelStruct), sigma = x$sigma, digits = digits, ...)
invisible(x)
}
diff --git a/R/saemix.R b/R/saemix.R
index 8955aa54..68bbd233 100644
--- a/R/saemix.R
+++ b/R/saemix.R
@@ -139,6 +139,36 @@ saem.mmkin <- function(object,
return(result)
}
+#' @export
+#' @rdname saem
+#' @param x An saem.mmkin object to print
+#' @param digits Number of digits to use for printing
+print.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...) {
+ cat( "Kinetic nonlinear mixed-effects model fit by SAEM" )
+ cat("\nStructural model:\n")
+ diffs <- x$mmkin[[1]]$mkinmod$diffs
+ nice_diffs <- gsub("^(d.*) =", "\\1/dt =", diffs)
+ writeLines(strwrap(nice_diffs, exdent = 11))
+ cat("\nData:\n")
+ cat(nrow(x$data), "observations of",
+ length(unique(x$data$name)), "variable(s) grouped in",
+ length(unique(x$data$ds)), "datasets\n")
+
+ cat("\nLikelihood computed by importance sampling\n")
+ print(data.frame(
+ AIC = AIC(x$so, type = "is"),
+ BIC = BIC(x$so, type = "is"),
+ logLik = logLik(x$so, type = "is"),
+ row.names = " "), digits = digits)
+
+ cat("\nFitted parameters:\n")
+ conf.int <- x$so@results@conf.int[c("estimate", "lower", "upper")]
+ rownames(conf.int) <- x$so@results@conf.int[["name"]]
+ print(conf.int, digits = digits)
+
+ invisible(x)
+}
+
#' @rdname saem
#' @return An [saemix::SaemixModel] object.
#' @export
diff --git a/R/summary.nlme.mmkin.R b/R/summary.nlme.mmkin.R
index ad730f9a..42326b39 100644
--- a/R/summary.nlme.mmkin.R
+++ b/R/summary.nlme.mmkin.R
@@ -191,10 +191,10 @@ print.summary.nlme.mmkin <- function(x, digits = max(3, getOption("digits") - 3)
cat("\nResults:\n\n")
print(data.frame(AIC = x$AIC, BIC = x$BIC, logLik = x$logLik,
- row.names = " "))
+ row.names = " "), ...)
cat("\nOptimised, transformed parameters with symmetric confidence intervals:\n")
- print(x$confint_trans)
+ print(x$confint_trans, digits = digits, ...)
if (nrow(x$confint_trans) > 1) {
corr <- x$corFixed
@@ -204,28 +204,28 @@ print.summary.nlme.mmkin <- function(x, digits = max(3, getOption("digits") - 3)
cat("\n") # Random effects
print(summary(x$modelStruct), sigma = x$sigma,
- reEstimates = x$coef$random, verbose = verbose, ...)
+ reEstimates = x$coef$random, digits = digits, verbose = verbose, ...)
cat("\nBacktransformed parameters with asymmetric confidence intervals:\n")
- print(x$confint_back)
+ print(x$confint_back, digits = digits, ...)
printSFORB <- !is.null(x$SFORB)
if(printSFORB){
cat("\nEstimated Eigenvalues of SFORB model(s):\n")
- print(x$SFORB, digits=digits,...)
+ print(x$SFORB, digits = digits,...)
}
printff <- !is.null(x$ff)
if(printff){
cat("\nResulting formation fractions:\n")
- print(data.frame(ff = x$ff), digits=digits,...)
+ print(data.frame(ff = x$ff), ...)
}
printdistimes <- !is.null(x$distimes)
if(printdistimes){
cat("\nEstimated disappearance times:\n")
- print(x$distimes, digits=digits,...)
+ print(x$distimes, digits = digits, ...)
}
if (x$print_data){
diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R
index 75fdb045..337120b2 100644
--- a/R/summary.saem.mmkin.R
+++ b/R/summary.saem.mmkin.R
@@ -213,10 +213,10 @@ print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3)
cat("\nResults:\n\n")
cat("Likelihood computed by importance sampling\n")
print(data.frame(AIC = x$AIC, BIC = x$BIC, logLik = x$logLik,
- row.names = " "))
+ row.names = " "), digits = digits)
cat("\nOptimised, transformed parameters with symmetric confidence intervals:\n")
- print(x$confint_trans)
+ print(x$confint_trans, digits = digits)
if (nrow(x$confint_trans) > 1) {
corr <- x$corFixed
@@ -225,30 +225,30 @@ print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3)
}
cat("\nRandom effects:\n")
- print(x$confint_ranef)
+ print(x$confint_ranef, digits = digits)
cat("\nVariance model:\n")
- print(x$confint_errmod)
+ print(x$confint_errmod, digits = digits)
cat("\nBacktransformed parameters with asymmetric confidence intervals:\n")
- print(x$confint_back)
+ print(x$confint_back, digits = digits)
printSFORB <- !is.null(x$SFORB)
if(printSFORB){
cat("\nEstimated Eigenvalues of SFORB model(s):\n")
- print(x$SFORB, digits=digits,...)
+ print(x$SFORB, digits = digits,...)
}
printff <- !is.null(x$ff)
if(printff){
cat("\nResulting formation fractions:\n")
- print(data.frame(ff = x$ff), digits=digits,...)
+ print(data.frame(ff = x$ff), digits = digits,...)
}
printdistimes <- !is.null(x$distimes)
if(printdistimes){
cat("\nEstimated disappearance times:\n")
- print(x$distimes, digits=digits,...)
+ print(x$distimes, digits = digits,...)
}
if (x$print_data){
diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index c068b8a4..3a868426 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -146,7 +146,8 @@
<a href="#mkin-0-9-50-4-unreleased" class="anchor"></a>mkin 0.9.50.4 (unreleased)<small> Unreleased </small>
</h1>
<ul>
-<li><p>‘saem’ generic function to fit saemix models, with a generator ‘saem.mmkin’ and further methods ‘summary.saem.mmkin’, ‘plot.saem.mmkin’</p></li>
+<li><p>‘plot.mixed.mmkin’ method used for ‘nlme.mmkin’ and ‘saem.mmkin’, both inheriting from ‘mixed.mmkin’ (currently virtual)</p></li>
+<li><p>‘saem’ generic function to fit saemix models, with a generator ‘saem.mmkin’, summary and plot methods</p></li>
<li><p>‘transform_odeparms’, ‘backtransform_odeparms’: Use logit transformation for solitary fractions like the g parameter of the DFOP model, or formation fractions for a pathway to only one target variable</p></li>
<li><p>‘update’ method for ‘mmkin’ objects</p></li>
<li><p>‘plot’, ‘summary’ and ‘print’ methods for ‘nlme.mmkin’ objects</p></li>
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index ef9bb681..17d7c266 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
web_only/NAFTA_examples: NAFTA_examples.html
web_only/benchmarks: benchmarks.html
web_only/compiled_models: compiled_models.html
-last_built: 2020-11-09T16:21Z
+last_built: 2020-11-10T04:11Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index ada9fb24..36c10225 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -325,7 +325,7 @@ of an mmkin object</p></td>
</tr><tr>
<td>
- <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> </p>
+ <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">print(<i>&lt;saem.mmkin&gt;</i>)</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> </p>
</td>
<td><p>Fit nonlinear mixed models with SAEM</p></td>
</tr><tr>
diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html
index defef75d..05edbde5 100644
--- a/docs/dev/reference/nlme.mmkin.html
+++ b/docs/dev/reference/nlme.mmkin.html
@@ -170,7 +170,7 @@ have been obtained by fitting the same model to a list of datasets.</p>
<span class='op'>)</span>
<span class='co'># S3 method for nlme.mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, digits <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"digits"</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>3</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='co'># S3 method for nlme.mmkin</span>
<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre>
@@ -242,6 +242,10 @@ parameters taken from the mmkin object are used</p></td>
<td><p>An nlme.mmkin object to print</p></td>
</tr>
<tr>
+ <th>digits</th>
+ <td><p>Number of digits to use for printing</p></td>
+ </tr>
+ <tr>
<th>...</th>
<td><p>Update specifications passed to update.nlme</p></td>
</tr>
@@ -262,8 +266,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
<code><a href='https://rdrr.io/pkg/nlme/man/intervals.html'>nlme::intervals()</a></code>, <code><a href='https://rdrr.io/pkg/nlme/man/anova.lme.html'>nlme::anova.lme()</a></code> and <code><a href='https://rdrr.io/pkg/nlme/man/coef.lme.html'>nlme::coef.lme()</a></code>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
- <div class='dont-index'><p><code><a href='nlme_function.html'>nlme_function()</a></code>, <a href='plot.mixed.mmkin.html'>plot.mixed.mmkin</a>, <a href='summary.nlme.mmkin.html'>summary.nlme.mmkin</a>,
-parms.nlme.mmkin</p></div>
+ <div class='dont-index'><p><code><a href='nlme_function.html'>nlme_function()</a></code>, <a href='plot.mixed.mmkin.html'>plot.mixed.mmkin</a>, <a href='summary.nlme.mmkin.html'>summary.nlme.mmkin</a></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
@@ -290,15 +293,15 @@ parms.nlme.mmkin</p></div>
#&gt;
#&gt; Fixed effects:
#&gt; list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)
-#&gt; parent_0 log_k1 log_k2 g_qlogis
-#&gt; 94.17015185 -1.80015278 -4.14738834 0.03239833
+#&gt; parent_0 log_k1 log_k2 g_qlogis
+#&gt; 94.1702 -1.8002 -4.1474 0.0324
#&gt;
#&gt; Random effects:
#&gt; Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)
#&gt; Level: ds
#&gt; Structure: Diagonal
-#&gt; parent_0 log_k1 log_k2 g_qlogis Residual
-#&gt; StdDev: 2.488249 0.8447275 1.32965 0.4651789 2.321364
+#&gt; parent_0 log_k1 log_k2 g_qlogis Residual
+#&gt; StdDev: 2.488 0.8447 1.33 0.4652 2.321
#&gt; </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
</div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $distimes
@@ -321,12 +324,12 @@ parms.nlme.mmkin</p></div>
#&gt; Fixed effects:
#&gt; list(parent_0 ~ 1, log_k_parent ~ 1)
#&gt; parent_0 log_k_parent
-#&gt; 75.933480 -3.555983
+#&gt; 75.933 -3.556
#&gt;
#&gt; Random effects:
#&gt; Formula: parent_0 ~ 1 | ds
-#&gt; parent_0 Residual
-#&gt; StdDev: 0.002416792 21.63027
+#&gt; parent_0 Residual
+#&gt; StdDev: 0.002417 21.63
#&gt; </div><div class='input'> <span class='va'>ds_2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
<span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span>
<span class='va'>m_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
@@ -427,15 +430,15 @@ parms.nlme.mmkin</p></div>
#&gt;
#&gt; Fixed effects:
#&gt; list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)
-#&gt; parent_0 log_k1 log_k2 g_qlogis
-#&gt; 94.04774566 -1.82339808 -4.16715311 0.05685186
+#&gt; parent_0 log_k1 log_k2 g_qlogis
+#&gt; 94.04775 -1.82340 -4.16715 0.05685
#&gt;
#&gt; Random effects:
#&gt; Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)
#&gt; Level: ds
#&gt; Structure: Diagonal
-#&gt; parent_0 log_k1 log_k2 g_qlogis Residual
-#&gt; StdDev: 2.473881 0.8499884 1.337185 0.4659005 1
+#&gt; parent_0 log_k1 log_k2 g_qlogis Residual
+#&gt; StdDev: 2.474 0.85 1.337 0.4659 1
#&gt;
#&gt; Variance function:
#&gt; Structure: Constant plus proportion of variance covariate
@@ -462,14 +465,14 @@ parms.nlme.mmkin</p></div>
#&gt; Fixed effects:
#&gt; list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1)
#&gt; parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink
-#&gt; 87.975536 -3.669816 -4.164127 -4.645073
+#&gt; 87.976 -3.670 -4.164 -4.645
#&gt;
#&gt; Random effects:
#&gt; Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1)
#&gt; Level: ds
#&gt; Structure: Diagonal
#&gt; parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink Residual
-#&gt; StdDev: 3.992214 1.77702 1.054733 0.4821383 6.482585
+#&gt; StdDev: 3.992 1.777 1.055 0.4821 6.483
#&gt;
#&gt; Variance function:
#&gt; Structure: Different standard deviations per stratum
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index f1b4c421..f9cdf1c8 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -164,6 +164,9 @@ Expectation Maximisation algorithm (SAEM).</p>
<span class='va'>...</span>
<span class='op'>)</span>
+<span class='co'># S3 method for saem.mmkin</span>
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, digits <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"digits"</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>3</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
+
<span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>object</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>object</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span></pre>
@@ -201,6 +204,14 @@ used.</p></td>
<td><p>Should we suppress any plotting that is done
by the saemix function?</p></td>
</tr>
+ <tr>
+ <th>x</th>
+ <td><p>An saem.mmkin object to print</p></td>
+ </tr>
+ <tr>
+ <th>digits</th>
+ <td><p>Number of digits to use for printing</p></td>
+ </tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -230,27 +241,27 @@ using <a href='mmkin.html'>mmkin</a>.</p>
state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>f_saem_p0_fixed</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 17:18:28 2020"
+#&gt; [1] "Tue Nov 10 05:12:21 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 17:18:30 2020"</div><div class='input'>
+#&gt; [1] "Tue Nov 10 05:12:23 2020"</div><div class='input'>
<span class='va'>f_mmkin_parent</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>f_saem_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</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><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 17:18:31 2020"
+#&gt; [1] "Tue Nov 10 05:12:24 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 17:18:33 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Tue Nov 10 05:12:26 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 17:18:33 2020"
+#&gt; [1] "Tue Nov 10 05:12:26 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 17:18:35 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Tue Nov 10 05:12:28 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 17:18:36 2020"
+#&gt; [1] "Tue Nov 10 05:12:29 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 17:18:39 2020"</div><div class='input'>
+#&gt; [1] "Tue Nov 10 05:12:32 2020"</div><div class='input'>
<span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span>
<span class='co'># functions from saemix</span>
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span>
@@ -296,10 +307,10 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='va'>f_mmkin_parent_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
<span class='va'>f_saem_fomc_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 17:18:41 2020"
+#&gt; [1] "Tue Nov 10 05:12:34 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 17:18:46 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
+#&gt; [1] "Tue Nov 10 05:12:39 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Likelihoods computed by importance sampling </div><div class='output co'>#&gt; AIC BIC
#&gt; 1 467.7644 465.0305
#&gt; 2 469.4862 466.3617</div><div class='input'>
@@ -319,20 +330,20 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='co'># solutions written for mkin this took around four minutes</span>
<span class='va'>f_saem_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 17:18:48 2020"
+#&gt; [1] "Tue Nov 10 05:12:42 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 17:18:53 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Tue Nov 10 05:12:47 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 17:18:54 2020"
+#&gt; [1] "Tue Nov 10 05:12:48 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 17:19:03 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
+#&gt; [1] "Tue Nov 10 05:12:57 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; saemix version used for fitting: 3.1.9000
#&gt; mkin version used for pre-fitting: 0.9.50.4
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Nov 9 17:19:04 2020
-#&gt; Date of summary: Mon Nov 9 17:19:04 2020
+#&gt; Date of fit: Tue Nov 10 05:12:58 2020
+#&gt; Date of summary: Tue Nov 10 05:12:58 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -347,7 +358,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 9.941 s using 300, 100 iterations
+#&gt; Fitted in 10.382 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Constant variance
#&gt;
@@ -363,17 +374,17 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; Results:
#&gt;
#&gt; Likelihood computed by importance sampling
-#&gt; AIC BIC logLik
-#&gt; 841.3208 836.2435 -407.6604
+#&gt; AIC BIC logLik
+#&gt; 841.3 836.2 -407.7
#&gt;
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; est. lower upper
-#&gt; parent_0 93.7514328489 91.113651 96.3892150
-#&gt; log_k_A1 -6.1262333211 -8.432492 -3.8199749
-#&gt; f_parent_qlogis -0.9739851652 -1.371984 -0.5759863
-#&gt; log_k1 -2.4818388836 -3.746899 -1.2167788
-#&gt; log_k2 -3.6138616567 -5.294149 -1.9335743
-#&gt; g_qlogis -0.0004613666 -1.063179 1.0622564
+#&gt; est. lower upper
+#&gt; parent_0 93.7514328 91.114 96.389
+#&gt; log_k_A1 -6.1262333 -8.432 -3.820
+#&gt; f_parent_qlogis -0.9739852 -1.372 -0.576
+#&gt; log_k1 -2.4818389 -3.747 -1.217
+#&gt; log_k2 -3.6138617 -5.294 -1.934
+#&gt; g_qlogis -0.0004614 -1.063 1.062
#&gt;
#&gt; Correlation:
#&gt; prnt_0 lg__A1 f_prn_ log_k1 log_k2
@@ -384,26 +395,26 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; g_qlogis -0.068 -0.016 0.011 -0.181 -0.181
#&gt;
#&gt; Random effects:
-#&gt; est. lower upper
-#&gt; SD.parent_0 2.7857084 0.7825105 4.7889063
-#&gt; SD.log_k_A1 2.1412505 0.4425207 3.8399803
-#&gt; SD.f_parent_qlogis 0.4463087 0.1609059 0.7317116
-#&gt; SD.log_k1 1.4097204 0.5240566 2.2953842
-#&gt; SD.log_k2 1.8739067 0.6979362 3.0498773
-#&gt; SD.g_qlogis 0.4559301 -0.8149852 1.7268453
+#&gt; est. lower upper
+#&gt; SD.parent_0 2.7857 0.7825 4.7889
+#&gt; SD.log_k_A1 2.1413 0.4425 3.8400
+#&gt; SD.f_parent_qlogis 0.4463 0.1609 0.7317
+#&gt; SD.log_k1 1.4097 0.5241 2.2954
+#&gt; SD.log_k2 1.8739 0.6979 3.0499
+#&gt; SD.g_qlogis 0.4559 -0.8150 1.7268
#&gt;
#&gt; Variance model:
-#&gt; est. lower upper
-#&gt; a.1 1.882757 1.665681 2.099832
+#&gt; est. lower upper
+#&gt; a.1 1.883 1.666 2.1
#&gt;
#&gt; Backtransformed parameters with asymmetric confidence intervals:
-#&gt; est. lower upper
-#&gt; parent_0 93.751432849 9.111365e+01 96.38921497
-#&gt; k_A1 0.002184795 2.176784e-04 0.02192835
-#&gt; f_parent_to_A1 0.274086887 2.022995e-01 0.35985666
-#&gt; k1 0.083589373 2.359079e-02 0.29618269
-#&gt; k2 0.026947583 5.020885e-03 0.14463032
-#&gt; g 0.499884658 2.567024e-01 0.74312150
+#&gt; est. lower upper
+#&gt; parent_0 93.751433 9.111e+01 96.38921
+#&gt; k_A1 0.002185 2.177e-04 0.02193
+#&gt; f_parent_to_A1 0.274087 2.023e-01 0.35986
+#&gt; k1 0.083589 2.359e-02 0.29618
+#&gt; k2 0.026948 5.021e-03 0.14463
+#&gt; g 0.499885 2.567e-01 0.74312
#&gt;
#&gt; Resulting formation fractions:
#&gt; ff
diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd
index 9526a427..abcd0e81 100644
--- a/man/nlme.mmkin.Rd
+++ b/man/nlme.mmkin.Rd
@@ -23,7 +23,7 @@
verbose = FALSE
)
-\method{print}{nlme.mmkin}(x, ...)
+\method{print}{nlme.mmkin}(x, digits = max(3, getOption("digits") - 3), ...)
\method{update}{nlme.mmkin}(object, ...)
}
@@ -61,6 +61,8 @@ parameters taken from the mmkin object are used}
\item{x}{An nlme.mmkin object to print}
+\item{digits}{Number of digits to use for printing}
+
\item{...}{Update specifications passed to update.nlme}
\item{object}{An nlme.mmkin object to update}
@@ -150,6 +152,5 @@ endpoints(f_nlme_dfop)
}
}
\seealso{
-\code{\link[=nlme_function]{nlme_function()}}, \link{plot.mixed.mmkin}, \link{summary.nlme.mmkin},
-\link{parms.nlme.mmkin}
+\code{\link[=nlme_function]{nlme_function()}}, \link{plot.mixed.mmkin}, \link{summary.nlme.mmkin}
}
diff --git a/man/saem.Rd b/man/saem.Rd
index 17f777c4..f75470a9 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -3,6 +3,7 @@
\name{saem}
\alias{saem}
\alias{saem.mmkin}
+\alias{print.saem.mmkin}
\alias{saemix_model}
\alias{saemix_data}
\title{Fit nonlinear mixed models with SAEM}
@@ -19,6 +20,8 @@ saem(object, control, ...)
...
)
+\method{print}{saem.mmkin}(x, digits = max(3, getOption("digits") - 3), ...)
+
saemix_model(object, cores = 1, verbose = FALSE, ...)
saemix_data(object, verbose = FALSE, ...)
@@ -41,6 +44,10 @@ used.}
\item{suppressPlot}{Should we suppress any plotting that is done
by the saemix function?}
+
+\item{x}{An saem.mmkin object to print}
+
+\item{digits}{Number of digits to use for printing}
}
\value{
An S3 object of class 'saem.mmkin', containing the fitted

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