Add plot method for saem.mmkin objects

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
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
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
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
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 -->
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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>
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+</div><!--/.navbar -->
+
+      
+
+      </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
+}