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-rw-r--r--NAMESPACE2
-rw-r--r--R/plot.saem.mmkin.R218
-rw-r--r--_pkgdown.yml1
-rw-r--r--docs/dev/pkgdown.yml2
-rw-r--r--docs/dev/reference/Rplot001.pngbin1011 -> 27839 bytes
-rw-r--r--docs/dev/reference/Rplot002.pngbin57363 -> 56909 bytes
-rw-r--r--docs/dev/reference/index.html6
-rw-r--r--docs/dev/reference/plot.nlme.mmkin.html10
-rw-r--r--docs/dev/reference/plot.saem.mmkin-1.pngbin0 -> 86076 bytes
-rw-r--r--docs/dev/reference/plot.saem.mmkin-2.pngbin0 -> 164014 bytes
-rw-r--r--docs/dev/reference/plot.saem.mmkin.html308
-rw-r--r--docs/dev/sitemap.xml3
-rw-r--r--man/plot.nlme.mmkin.Rd8
-rw-r--r--man/plot.saem.mmkin.Rd94
14 files changed, 637 insertions, 15 deletions
diff --git a/NAMESPACE b/NAMESPACE
index ed1a46de..29462082 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -20,6 +20,7 @@ S3method(plot,mkinfit)
S3method(plot,mmkin)
S3method(plot,nafta)
S3method(plot,nlme.mmkin)
+S3method(plot,saem.mmkin)
S3method(print,mkinds)
S3method(print,mkinmod)
S3method(print,mmkin)
@@ -98,6 +99,7 @@ importFrom(parallel,mclapply)
importFrom(parallel,parLapply)
importFrom(pkgbuild,has_compiler)
importFrom(purrr,map_dfr)
+importFrom(saemix,psi)
importFrom(stats,AIC)
importFrom(stats,BIC)
importFrom(stats,aggregate)
diff --git a/R/plot.saem.mmkin.R b/R/plot.saem.mmkin.R
new file mode 100644
index 00000000..ce43fdb6
--- /dev/null
+++ b/R/plot.saem.mmkin.R
@@ -0,0 +1,218 @@
+if(getRversion() >= '2.15.1') utils::globalVariables("ds")
+
+#' Plot an saem fitted nonlinear mixed model obtained via an mmkin row object
+#'
+#' @param x An object of class \code{\link{saem.mmkin}}
+#' @param i A numeric index to select datasets for which to plot the saem fit,
+#' in case plots get too large
+#' @inheritParams plot.mkinfit
+#' @param standardized Should the residuals be standardized? Only takes effect if
+#' `resplot = "time"`.
+#' @param rel.height.legend The relative height of the legend shown on top
+#' @param rel.height.bottom The relative height of the bottom plot row
+#' @param ymax Vector of maximum y axis values
+#' @param ncol.legend Number of columns to use in the legend
+#' @param nrow.legend Number of rows to use in the legend
+#' @param resplot Should the residuals plotted against time or against
+#' predicted values?
+#' @param col_ds Colors used for plotting the observed data and the
+#' corresponding model prediction lines for the different datasets.
+#' @param pch_ds Symbols to be used for plotting the data.
+#' @param lty_ds Line types to be used for the model predictions.
+#' @importFrom saemix psi
+#' @return The function is called for its side effect.
+#' @author Johannes Ranke
+#' @examples
+#' ds <- lapply(experimental_data_for_UBA_2019[6:10],
+#' function(x) x$data[c("name", "time", "value")])
+#' names(ds) <- paste0("ds ", 6:10)
+#' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
+#' A1 = mkinsub("SFO"), quiet = TRUE)
+#' \dontrun{
+#' f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE)
+#' plot(f[, 3:4], standardized = TRUE)
+#'
+#' f_saem <- saem(f)
+#' plot(f_saem)
+#' }
+#' @export
+plot.saem.mmkin <- function(x, i = 1:ncol(x$mmkin),
+ obs_vars = names(x$mkinmod$map),
+ standardized = TRUE,
+ xlab = "Time",
+ xlim = range(x$data$time),
+ resplot = c("predicted", "time"),
+ ymax = "auto", maxabs = "auto",
+ ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
+ nrow.legend = ceiling((length(i) + 1) / ncol.legend),
+ rel.height.legend = 0.03 + 0.08 * nrow.legend,
+ rel.height.bottom = 1.1,
+ pch_ds = 1:length(i),
+ col_ds = pch_ds + 1,
+ lty_ds = col_ds,
+ frame = TRUE, ...)
+{
+
+ oldpar <- par(no.readonly = TRUE)
+
+ fit_1 <- x$mmkin[[1]]
+ ds_names <- colnames(x$mmkin)
+
+ degparms_optim <- psi(x$so)
+ rownames(degparms_optim) <- ds_names
+ degparms_optim_names <- setdiff(names(fit_1$par), names(fit_1$errparms))
+ colnames(degparms_optim) <- degparms_optim_names
+
+ degparms_fixed <- fit_1$fixed$value
+ names(degparms_fixed) <- rownames(fit_1$fixed)
+ degparms_all <- cbind(as.matrix(degparms_optim),
+ matrix(rep(degparms_fixed, nrow(degparms_optim)),
+ ncol = length(degparms_fixed),
+ nrow = nrow(degparms_optim), byrow = TRUE))
+ degparms_all_names <- c(degparms_optim_names, names(degparms_fixed))
+ colnames(degparms_all) <- degparms_all_names
+
+ odeini_names <- grep("_0$", degparms_all_names, value = TRUE)
+ odeparms_names <- setdiff(degparms_all_names, odeini_names)
+
+ residual_type = ifelse(standardized, "iwres", "ires")
+
+ observed <- cbind(x$data,
+ residual = x$so@results@predictions[[residual_type]])
+
+ n_plot_rows = length(obs_vars)
+ n_plots = n_plot_rows * 2
+
+ # Set relative plot heights, so the first plot row is the norm
+ rel.heights <- if (n_plot_rows > 1) {
+ c(rel.height.legend, c(rep(1, n_plot_rows - 1), rel.height.bottom))
+ } else {
+ c(rel.height.legend, 1)
+ }
+
+ layout_matrix = matrix(c(1, 1, 2:(n_plots + 1)),
+ n_plot_rows + 1, 2, byrow = TRUE)
+ layout(layout_matrix, heights = rel.heights)
+
+ par(mar = c(0.1, 2.1, 0.6, 2.1))
+
+ plot(0, type = "n", axes = FALSE, ann = FALSE)
+ legend("center", bty = "n", ncol = ncol.legend,
+ legend = c("Population", ds_names[i]),
+ lty = c(1, lty_ds), lwd = c(2, rep(1, length(i))),
+ col = c(1, col_ds),
+ pch = c(NA, pch_ds))
+
+
+ solution_type = fit_1$solution_type
+
+ outtimes <- sort(unique(c(x$data$time,
+ seq(xlim[1], xlim[2], length.out = 50))))
+
+ pred_ds <- purrr::map_dfr(i, function(ds_i) {
+ odeparms_trans <- degparms_all[ds_i, odeparms_names]
+ names(odeparms_trans) <- odeparms_names # needed if only one odeparm
+ odeparms <- backtransform_odeparms(odeparms_trans,
+ x$mkinmod,
+ transform_rates = fit_1$transform_rates,
+ transform_fractions = fit_1$transform_fractions)
+
+ odeini <- degparms_all[ds_i, odeini_names]
+ names(odeini) <- gsub("_0", "", odeini_names)
+
+ out <- mkinpredict(x$mkinmod, odeparms, odeini,
+ outtimes, solution_type = solution_type,
+ atol = fit_1$atol, rtol = fit_1$rtol)
+ return(cbind(as.data.frame(out), ds = ds_names[ds_i]))
+ })
+
+ degparms_pop <- x$so@results@fixed.effects
+ names(degparms_pop) <- degparms_optim_names
+ degparms_all_pop <- c(degparms_pop, degparms_fixed)
+
+ odeparms_pop_trans <- degparms_all_pop[odeparms_names]
+ odeparms_pop <- backtransform_odeparms(odeparms_pop_trans,
+ x$mkinmod,
+ transform_rates = fit_1$transform_rates,
+ transform_fractions = fit_1$transform_fractions)
+
+ odeini_pop <- degparms_all_pop[odeini_names]
+ names(odeini_pop) <- gsub("_0", "", odeini_names)
+
+ pred_pop <- as.data.frame(
+ mkinpredict(x$mkinmod, odeparms_pop, odeini_pop,
+ outtimes, solution_type = solution_type,
+ atol = fit_1$atol, rtol = fit_1$rtol))
+
+ resplot <- match.arg(resplot)
+
+ # Loop plot rows
+ for (plot_row in 1:n_plot_rows) {
+
+ obs_var <- obs_vars[plot_row]
+ observed_row <- subset(observed, name == obs_var)
+
+ # Set ylim to sensible default, or use ymax
+ if (identical(ymax, "auto")) {
+ ylim_row = c(0,
+ max(c(observed_row$value, pred_ds[[obs_var]]), na.rm = TRUE))
+ } else {
+ ylim_row = c(0, ymax[plot_row])
+ }
+
+ # Margins for bottom row of plots when we have more than one row
+ # This is the only row that needs to show the x axis legend
+ if (plot_row == n_plot_rows) {
+ par(mar = c(5.1, 4.1, 2.1, 2.1))
+ } else {
+ par(mar = c(3.0, 4.1, 2.1, 2.1))
+ }
+
+ plot(pred_pop$time, pred_pop[[obs_var]],
+ type = "l", lwd = 2,
+ xlim = xlim, ylim = ylim_row,
+ xlab = xlab, ylab = obs_var, frame = frame)
+
+ for (ds_i in seq_along(i)) {
+ points(subset(observed_row, ds == ds_names[ds_i], c("time", "value")),
+ col = col_ds[ds_i], pch = pch_ds[ds_i])
+ lines(subset(pred_ds, ds == ds_names[ds_i], c("time", obs_var)),
+ col = col_ds[ds_i], lty = lty_ds[ds_i])
+ }
+
+ if (identical(maxabs, "auto")) {
+ maxabs = max(abs(observed_row$residual), na.rm = TRUE)
+ }
+
+ if (identical(resplot, "time")) {
+ plot(0, type = "n", xlim = xlim, xlab = "Time",
+ ylim = c(-1.2 * maxabs, 1.2 * maxabs),
+ ylab = if (standardized) "Standardized residual" else "Residual")
+
+ abline(h = 0, lty = 2)
+
+ for (ds_i in seq_along(i)) {
+ points(subset(observed_row, ds == ds_names[ds_i], c("time", "residual")),
+ col = col_ds[ds_i], pch = pch_ds[ds_i])
+ }
+ }
+
+ if (identical(resplot, "predicted")) {
+ plot(0, type = "n",
+ xlim = c(0, max(pred_ds[[obs_var]])),
+ xlab = "Predicted",
+ ylim = c(-1.2 * maxabs, 1.2 * maxabs),
+ ylab = if (standardized) "Standardized residual" else "Residual")
+
+ abline(h = 0, lty = 2)
+
+ for (ds_i in seq_along(i)) {
+ observed_row_ds <- merge(
+ subset(observed_row, ds == ds_names[ds_i], c("time", "residual")),
+ subset(pred_ds, ds == ds_names[ds_i], c("time", obs_var)))
+ points(observed_row_ds[c(3, 2)],
+ col = col_ds[ds_i], pch = pch_ds[ds_i])
+ }
+ }
+ }
+}
diff --git a/_pkgdown.yml b/_pkgdown.yml
index b036ed59..61c69a9d 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -46,6 +46,7 @@ reference:
- summary.nlme.mmkin
- saem.mmkin
- summary.saem.mmkin
+ - plot.saem.mmkin
- nlme_function
- get_deg_func
- saemix_model
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index a8bb6144..e14af5e0 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: 2020-11-09T08:23Z
+last_built: 2020-11-09T13:23Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index 17a35806..cfc5bc2b 100644
--- a/docs/dev/reference/Rplot001.png
+++ b/docs/dev/reference/Rplot001.png
Binary files differ
diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png
index 8ada7133..cd2014eb 100644
--- a/docs/dev/reference/Rplot002.png
+++ b/docs/dev/reference/Rplot002.png
Binary files differ
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index 825c4d27..f5621402 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -349,6 +349,12 @@ of an mmkin object</p></td>
</tr><tr>
<td>
+ <p><code><a href="plot.saem.mmkin.html">plot(<i>&lt;saem.mmkin&gt;</i>)</a></code> </p>
+ </td>
+ <td><p>Plot an saem fitted nonlinear mixed model obtained via an mmkin row object</p></td>
+ </tr><tr>
+
+ <td>
<p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">mean_degparms()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p>
</td>
<td><p>Helper functions to create nlme models from mmkin row objects</p></td>
diff --git a/docs/dev/reference/plot.nlme.mmkin.html b/docs/dev/reference/plot.nlme.mmkin.html
index 267bef05..8f5f85f7 100644
--- a/docs/dev/reference/plot.nlme.mmkin.html
+++ b/docs/dev/reference/plot.nlme.mmkin.html
@@ -150,7 +150,7 @@
<pre class="usage"><span class='co'># S3 method for nlme.mmkin</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
<span class='va'>x</span>,
- i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin_orig</span><span class='op'>)</span>,
+ i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>,
obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
@@ -165,8 +165,7 @@
pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>,
col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>,
lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>,
- frame <span class='op'>=</span> <span class='cn'>TRUE</span>,
- <span class='va'>...</span>
+ frame <span class='op'>=</span> <span class='cn'>TRUE</span>
<span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -247,11 +246,6 @@ corresponding model prediction lines for the different datasets.</p></td>
<th>frame</th>
<td><p>Should a frame be drawn around the plots?</p></td>
</tr>
- <tr>
- <th>...</th>
- <td><p>Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and
-<code><a href='mkinresplot.html'>mkinresplot</a></code>.</p></td>
- </tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
diff --git a/docs/dev/reference/plot.saem.mmkin-1.png b/docs/dev/reference/plot.saem.mmkin-1.png
new file mode 100644
index 00000000..5cb33214
--- /dev/null
+++ b/docs/dev/reference/plot.saem.mmkin-1.png
Binary files differ
diff --git a/docs/dev/reference/plot.saem.mmkin-2.png b/docs/dev/reference/plot.saem.mmkin-2.png
new file mode 100644
index 00000000..67058e6c
--- /dev/null
+++ b/docs/dev/reference/plot.saem.mmkin-2.png
Binary files differ
diff --git a/docs/dev/reference/plot.saem.mmkin.html b/docs/dev/reference/plot.saem.mmkin.html
new file mode 100644
index 00000000..d0790a98
--- /dev/null
+++ b/docs/dev/reference/plot.saem.mmkin.html
@@ -0,0 +1,308 @@
+<!-- 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>Plot an saem fitted nonlinear mixed model obtained via an mmkin row object — plot.saem.mmkin • mkin</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
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+
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+
+<meta property="og:title" content="Plot an saem fitted nonlinear mixed model obtained via an mmkin row object — plot.saem.mmkin" />
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+<![endif]-->
+
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+
+ </head>
+
+ <body data-spy="scroll" data-target="#toc">
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
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+ <span class="icon-bar"></span>
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+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">mkin</a>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Functions and data</a>
+</li>
+<li class="dropdown">
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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>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
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+ <span class="fab fa fab fa-github fa-lg"></span>
+
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+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
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+
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+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Plot an saem fitted nonlinear mixed model obtained via an mmkin row object</h1>
+ <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.saem.mmkin.R'><code>R/plot.saem.mmkin.R</code></a></small>
+ <div class="hidden name"><code>plot.saem.mmkin.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Plot an saem fitted nonlinear mixed model obtained via an mmkin row object</p>
+ </div>
+
+ <pre class="usage"><span class='co'># S3 method for saem.mmkin</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
+ <span class='va'>x</span>,
+ i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>,
+ obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
+ standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
+ xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
+ xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>,
+ resplot <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'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>,
+ ymax <span class='op'>=</span> <span class='st'>"auto"</span>,
+ maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
+ ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>,
+ nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>,
+ rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>,
+ rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>,
+ pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>,
+ col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>,
+ lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>,
+ frame <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>x</th>
+ <td><p>An object of class <code><a href='saem.html'>saem.mmkin</a></code></p></td>
+ </tr>
+ <tr>
+ <th>i</th>
+ <td><p>A numeric index to select datasets for which to plot the saem fit,
+in case plots get too large</p></td>
+ </tr>
+ <tr>
+ <th>obs_vars</th>
+ <td><p>A character vector of names of the observed variables for
+which the data and the model should be plotted. Defauls to all observed
+variables in the model.</p></td>
+ </tr>
+ <tr>
+ <th>standardized</th>
+ <td><p>Should the residuals be standardized? Only takes effect if
+<code>resplot = "time"</code>.</p></td>
+ </tr>
+ <tr>
+ <th>xlab</th>
+ <td><p>Label for the x axis.</p></td>
+ </tr>
+ <tr>
+ <th>xlim</th>
+ <td><p>Plot range in x direction.</p></td>
+ </tr>
+ <tr>
+ <th>resplot</th>
+ <td><p>Should the residuals plotted against time or against
+predicted values?</p></td>
+ </tr>
+ <tr>
+ <th>ymax</th>
+ <td><p>Vector of maximum y axis values</p></td>
+ </tr>
+ <tr>
+ <th>maxabs</th>
+ <td><p>Maximum absolute value of the residuals. This is used for the
+scaling of the y axis and defaults to "auto".</p></td>
+ </tr>
+ <tr>
+ <th>ncol.legend</th>
+ <td><p>Number of columns to use in the legend</p></td>
+ </tr>
+ <tr>
+ <th>nrow.legend</th>
+ <td><p>Number of rows to use in the legend</p></td>
+ </tr>
+ <tr>
+ <th>rel.height.legend</th>
+ <td><p>The relative height of the legend shown on top</p></td>
+ </tr>
+ <tr>
+ <th>rel.height.bottom</th>
+ <td><p>The relative height of the bottom plot row</p></td>
+ </tr>
+ <tr>
+ <th>pch_ds</th>
+ <td><p>Symbols to be used for plotting the data.</p></td>
+ </tr>
+ <tr>
+ <th>col_ds</th>
+ <td><p>Colors used for plotting the observed data and the
+corresponding model prediction lines for the different datasets.</p></td>
+ </tr>
+ <tr>
+ <th>lty_ds</th>
+ <td><p>Line types to be used for the model predictions.</p></td>
+ </tr>
+ <tr>
+ <th>frame</th>
+ <td><p>Should a frame be drawn around the plots?</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The function is called for its side effect.</p>
+ <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+ <p>Johannes Ranke</p>
+
+ <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>,
+ <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='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"ds "</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span>
+<span class='va'>dfop_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'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
+ A1 <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='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='co'># \dontrun{</span>
+<span class='va'>f</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/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</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='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='img'><img src='plot.saem.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='va'>f_saem</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Running main SAEM algorithm
+#&gt; [1] "Mon Nov 9 14:21:22 2020"
+#&gt; ....
+#&gt; Minimisation finished
+#&gt; [1] "Mon Nov 9 14:21:31 2020"</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_saem</span><span class='op'>)</span>
+</div><div class='img'><img src='plot.saem.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
+</div></pre>
+ </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>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml
index d9ef2228..d6f55550 100644
--- a/docs/dev/sitemap.xml
+++ b/docs/dev/sitemap.xml
@@ -160,6 +160,9 @@
<loc>https://pkgdown.jrwb.de/mkin/reference/plot.nlme.mmkin.html</loc>
</url>
<url>
+ <loc>https://pkgdown.jrwb.de/mkin/reference/plot.saem.mmkin.html</loc>
+ </url>
+ <url>
<loc>https://pkgdown.jrwb.de/mkin/reference/print.mkinds.html</loc>
</url>
<url>
diff --git a/man/plot.nlme.mmkin.Rd b/man/plot.nlme.mmkin.Rd
index 5f0f0ef1..f426f77b 100644
--- a/man/plot.nlme.mmkin.Rd
+++ b/man/plot.nlme.mmkin.Rd
@@ -6,7 +6,7 @@
\usage{
\method{plot}{nlme.mmkin}(
x,
- i = 1:ncol(x$mmkin_orig),
+ i = 1:ncol(x$mmkin),
obs_vars = names(x$mkinmod$map),
standardized = TRUE,
xlab = "Time",
@@ -21,8 +21,7 @@
pch_ds = 1:length(i),
col_ds = pch_ds + 1,
lty_ds = col_ds,
- frame = TRUE,
- ...
+ frame = TRUE
)
}
\arguments{
@@ -66,9 +65,6 @@ corresponding model prediction lines for the different datasets.}
\item{lty_ds}{Line types to be used for the model predictions.}
\item{frame}{Should a frame be drawn around the plots?}
-
-\item{\dots}{Further arguments passed to \code{\link{plot.mkinfit}} and
-\code{\link{mkinresplot}}.}
}
\value{
The function is called for its side effect.
diff --git a/man/plot.saem.mmkin.Rd b/man/plot.saem.mmkin.Rd
new file mode 100644
index 00000000..1f674bd7
--- /dev/null
+++ b/man/plot.saem.mmkin.Rd
@@ -0,0 +1,94 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot.saem.mmkin.R
+\name{plot.saem.mmkin}
+\alias{plot.saem.mmkin}
+\title{Plot an saem fitted nonlinear mixed model obtained via an mmkin row object}
+\usage{
+\method{plot}{saem.mmkin}(
+ x,
+ i = 1:ncol(x$mmkin),
+ obs_vars = names(x$mkinmod$map),
+ standardized = TRUE,
+ xlab = "Time",
+ xlim = range(x$data$time),
+ resplot = c("predicted", "time"),
+ ymax = "auto",
+ maxabs = "auto",
+ ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
+ nrow.legend = ceiling((length(i) + 1)/ncol.legend),
+ rel.height.legend = 0.03 + 0.08 * nrow.legend,
+ rel.height.bottom = 1.1,
+ pch_ds = 1:length(i),
+ col_ds = pch_ds + 1,
+ lty_ds = col_ds,
+ frame = TRUE,
+ ...
+)
+}
+\arguments{
+\item{x}{An object of class \code{\link{saem.mmkin}}}
+
+\item{i}{A numeric index to select datasets for which to plot the saem fit,
+in case plots get too large}
+
+\item{obs_vars}{A character vector of names of the observed variables for
+which the data and the model should be plotted. Defauls to all observed
+variables in the model.}
+
+\item{standardized}{Should the residuals be standardized? Only takes effect if
+\code{resplot = "time"}.}
+
+\item{xlab}{Label for the x axis.}
+
+\item{xlim}{Plot range in x direction.}
+
+\item{resplot}{Should the residuals plotted against time or against
+predicted values?}
+
+\item{ymax}{Vector of maximum y axis values}
+
+\item{maxabs}{Maximum absolute value of the residuals. This is used for the
+scaling of the y axis and defaults to "auto".}
+
+\item{ncol.legend}{Number of columns to use in the legend}
+
+\item{nrow.legend}{Number of rows to use in the legend}
+
+\item{rel.height.legend}{The relative height of the legend shown on top}
+
+\item{rel.height.bottom}{The relative height of the bottom plot row}
+
+\item{pch_ds}{Symbols to be used for plotting the data.}
+
+\item{col_ds}{Colors used for plotting the observed data and the
+corresponding model prediction lines for the different datasets.}
+
+\item{lty_ds}{Line types to be used for the model predictions.}
+
+\item{frame}{Should a frame be drawn around the plots?}
+
+\item{...}{Further arguments passed to \code{\link{plot}}.}
+}
+\value{
+The function is called for its side effect.
+}
+\description{
+Plot an saem fitted nonlinear mixed model obtained via an mmkin row object
+}
+\examples{
+ds <- lapply(experimental_data_for_UBA_2019[6:10],
+ function(x) x$data[c("name", "time", "value")])
+names(ds) <- paste0("ds ", 6:10)
+dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
+ A1 = mkinsub("SFO"), quiet = TRUE)
+\dontrun{
+f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE)
+plot(f[, 3:4], standardized = TRUE)
+
+f_saem <- saem(f)
+plot(f_saem)
+}
+}
+\author{
+Johannes Ranke
+}

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