Plot method for nlme.mmkin objects

Update docs

20 files changed, 624 insertions, 189 deletions

diff --git a/NAMESPACE b/NAMESPACE
index 0a04d6c3..645c145e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -22,6 +22,7 @@ S3method(plot,nafta)
 S3method(plot,nlme.mmkin)
 S3method(print,mkinds)
 S3method(print,mkinmod)
+S3method(print,mmkin)
 S3method(print,nafta)
 S3method(print,nlme.mmkin)
 S3method(print,summary.mkinfit)
diff --git a/NEWS.md b/NEWS.md
index b7e8f38c..ea4b5318 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,7 @@
 # mkin 0.9.50.4 (unreleased)
 
+- 'plot' method for 'nlme.mmkin' objects
+
 - 'print' method for 'mmkin' objects
 
 - 'saemix_model', 'saemix_data': Helper functions to fit nonlinear mixed-effects models for mmkin row objects using the saemix package
diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R
index c8a99d59..d4720e79 100644
--- a/R/nlme.mmkin.R
+++ b/R/nlme.mmkin.R
@@ -196,6 +196,8 @@ nlme.mmkin <- function(model, data = sys.frame(sys.parent()),
 
   val <- do.call("nlme.formula", thisCall)
   val$mmkin_orig <- model
+  val$data <- thisCall[["data"]]
+  val$mkinmod <- model[[1]]$mkinmod
   class(val) <- c("nlme.mmkin", "nlme", "lme")
   return(val)
 }
diff --git a/R/plot.mmkin.R b/R/plot.mmkin.R
index ac66e542..0523e4d3 100644
--- a/R/plot.mmkin.R
+++ b/R/plot.mmkin.R
@@ -54,12 +54,16 @@
 #'
 #' @export
 plot.mmkin <- function(x, main = "auto", legends = 1,
-                       resplot = c("time", "errmod"),
-                       standardized = FALSE,
-                       show_errmin = TRUE,
-                       errmin_var = "All data", errmin_digits = 3,
-                       cex = 0.7, rel.height.middle = 0.9,
-                       ymax = "auto", ...) {
+  resplot = c("time", "errmod"),
+  standardized = FALSE,
+  show_errmin = TRUE,
+  errmin_var = "All data", errmin_digits = 3,
+  cex = 0.7, rel.height.middle = 0.9,
+  ymax = "auto", ...)
+{
+
+  oldpar <- par(no.readonly = TRUE)
+
   n.m <- nrow(x)
   n.d <- ncol(x)
 
@@ -82,8 +86,6 @@ plot.mmkin <- function(x, main = "auto", legends = 1,
                   datasets = rownames(x))
   }
 
-  oldpar <- par(no.readonly = TRUE)
-
   # Set relative plot heights, so the first and the last plot are the norm
   # and the middle plots (if n.fits >2) are smaller by rel.height.middle
   rel.heights <- if (n.fits > 2) c(1, rep(rel.height.middle, n.fits - 2), 1)
diff --git a/R/plot.nlme.mmkin.R b/R/plot.nlme.mmkin.R
index 0f3ad715..084099ac 100644
--- a/R/plot.nlme.mmkin.R
+++ b/R/plot.nlme.mmkin.R
@@ -1,115 +1,224 @@
+if(getRversion() >= '2.15.1') utils::globalVariables("ds")
+
 #' Plot a fitted nonlinear mixed model obtained via an mmkin row object
 #'
 #' @param x An object of class \code{\link{nlme.mmkin}}
 #' @param i A numeric index to select datasets for which to plot the nlme fit,
 #'   in case plots get too large
 #' @param main The main title placed on the outer margin of the plot.
+#' @inheritParams plot.mkinfit
 #' @param legends An index for the fits for which legends should be shown.
-#' @param resplot Should the residuals plotted against time, using
-#'   \code{\link{mkinresplot}}, or as squared residuals against predicted
-#'   values, with the error model, using \code{\link{mkinerrplot}}.
-#' @param standardized Should the residuals be standardized? This option
-#'   is passed to \code{\link{mkinresplot}}, it only takes effect if
+#' @param standardized Should the residuals be standardized? Only takes effect if
 #'   `resplot = "time"`.
-#' @param show_errmin Should the chi2 error level be shown on top of the plots
-#'   to the left?
-#' @param errmin_var The variable for which the FOCUS chi2 error value should
-#'   be shown.
-#' @param errmin_digits The number of significant digits for rounding the FOCUS
-#'   chi2 error percentage.
 #' @param cex Passed to the plot functions and \code{\link{mtext}}.
 #' @param rel.height.middle The relative height of the middle plot, if more
 #'   than two rows of plots are shown.
-#' @param ymax Maximum y axis value for \code{\link{plot.mkinfit}}.
+#' @param ymax Vector of maximum y axis values
 #' @param \dots Further arguments passed to \code{\link{plot.mkinfit}} and
 #'   \code{\link{mkinresplot}}.
+#' @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 stats coefficients
 #' @return The function is called for its side effect.
 #' @author Johannes Ranke
 #' @examples
 #' ds <- lapply(experimental_data_for_UBA_2019[6:10],
-#'  function(x) subset(x$data[c("name", "time", "value")], name == "parent"))
-#' f <- mmkin("SFO", ds, quiet = TRUE, cores = 1)
-#' #plot(f) # too many panels for pkgdown
-#' plot(f[, 3:4])
+#'  function(x) x$data[c("name", "time", "value")])
+#' names(ds) <- paste0("ds ", 6:10)
+#' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
+#'   A1 = mkinsub("SFO"), quiet = TRUE)
+#' f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, cores = 1)
+#' plot(f[, 3:4], standardized = TRUE)
 #' library(nlme)
-#' f_nlme <- nlme(f)
-#'
-#' #plot(f_nlme) # too many panels for pkgdown
-#' plot(f_nlme, 3:4)
+#' # For this fit we need to increase pnlsMaxiter, and we increase the
+#' # tolerance in order to speed up the fit for this example evaluation
+#' f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-4))
+#' plot(f_nlme)
 #' @export
 plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig),
-  main = "auto", legends = 1,
-  resplot = c("time", "errmod"),
-  standardized = FALSE,
-  show_errmin = TRUE,
-  errmin_var = "All data", errmin_digits = 3,
+  main = rownames(x$mmkin_orig),
+  obs_vars = names(x$mkinmod$map),
+  standardized = TRUE,
+  xlab = "Time", ylab = "Observed",
+  xlim = range(x$data$time),
+  legends = 1,
+  lpos = "topright", inset = c(0.05, 0.05),
+  resplot = c("predicted", "time"),
+  ymax = "auto", maxabs = "auto",
   cex = 0.7, rel.height.middle = 0.9,
-  ymax = "auto", ...)
+  pch_ds = 1:length(i),
+  col_ds = pch_ds + 1,
+  lty_ds = col_ds,
+  frame = TRUE, ...)
 {
 
-  degparms_optim_nlme <- coefficients(x)
-  degparms_optim_names <- names(degparms_optim_nlme)
+  oldpar <- par(no.readonly = TRUE)
 
-  odeini_optim_names <- grep("_0$", degparms_optim_names, value = TRUE)
-  odeparms_optim_names <- setdiff(degparms_optim_names, odeini_optim_names)
+  fit_1 = x$mmkin_orig[[1]]
+  ds_names <- colnames(x$mmkin_orig)
 
-  fit_1 <- x$mmkin_orig[[1]]
+  degparms_optim <- coefficients(x)
+  degparms_optim_names <- names(degparms_optim)
+  degparms_fixed <- fit_1$fixed$value
+  names(degparms_fixed) <- rownames(fit_1$fixed)
+  degparms_all <- cbind(as.matrix(degparms_optim), fit_1$bparms.fixed)
+  degparms_all_names <- c(degparms_optim_names, names(degparms_fixed))
+  colnames(degparms_all) <- degparms_all_names
 
-  mkinfit_call <- as.list(fit_1$call)[-1]
-  mkinfit_call[["mkinmod"]] <- fit_1$mkinmod
+  odeini_names <- grep("_0$", degparms_all_names, value = TRUE)
+  odeparms_names <- setdiff(degparms_all_names, odeini_names)
 
-  ds <- lapply(x$mmkin_orig, function(x) {
-    data.frame(name = x$data$variable,
-      time = x$data$time,
-      value = x$data$observed)
-  })
+  residual_type = ifelse(standardized, "pearson", "response")
 
-  # This takes quite some time. This could be greatly reduced
-  # if the plot.mkinfit code would be imported and adapted,
-  # allowing also to overly plots of mmkin fits and nlme fits
-  mmkin_nlme <- lapply(i, function(a) {
+  observed <- cbind(x$data,
+    residual = residuals(x, type = residual_type))
 
-    degparms_optim <- as.numeric(degparms_optim_nlme[a, ])
-    names(degparms_optim) <- degparms_optim_names
+  n_plot_rows = length(obs_vars)
+  n_plots = n_plot_rows * 2
 
-    odeini_optim <- degparms_optim[odeini_optim_names]
-    names(odeini_optim) <- gsub("_0$", "", names(odeini_optim))
-
-    odeparms_optim_trans <- degparms_optim[odeparms_optim_names]
-    odeparms_optim <- backtransform_odeparms(odeparms_optim_trans,
-      fit_1$mkinmod,
-      transform_rates = fit_1$transform_rates,
-      transform_fractions = fit_1$transform_fractions)
+  # Set relative plot heights, so the first and the last plot are the norm
+  # and the middle plots (if n_plot_rows >2) are smaller by rel.height.middle
+  rel.heights <- if (n_plot_rows > 2) {
+    c(1, rep(rel.height.middle, n_plot_rows - 2), 1)
+  } else {
+    rep(1, n_plot_rows)
+  }
 
-    fit_a <- x$mmkin_orig[[a]]
+  layout_matrix = matrix(1:n_plots,
+    n_plot_rows, 2, byrow = TRUE)
+  layout(layout_matrix, heights = rel.heights)
 
-    state_ini <- fit_a$bparms.state
-    state_ini[names(odeini_optim)] <- odeini_optim
+  solution_type = fit_1$solution_type
 
-    odeparms <- fit_a$bparms.ode
-    odeparms[names(odeparms_optim)] <- odeparms_optim
+  outtimes <- sort(unique(c(x$data$time,
+    seq(xlim[1], xlim[2], length.out = 50))))
 
-    mkinfit_call[["observed"]] <- ds[[a]]
-    mkinfit_call[["parms.ini"]] <- odeparms
-    mkinfit_call[["state.ini"]] <- state_ini
+  pred_ds <- purrr::map_dfr(i, function(ds_i)   {
+    odeparms_trans <- degparms_all[ds_i, odeparms_names]
+    odeparms <- backtransform_odeparms(odeparms_trans,
+      x$mkinmod,
+      transform_rates = fit_1$transform_rates,
+      transform_fractions = fit_1$transform_fractions)
 
-    mkinfit_call[["control"]] <- list(iter.max = 0)
-    mkinfit_call[["quiet"]] <- TRUE
+    odeini <- degparms_all[ds_i, odeini_names]
+    names(odeini) <- gsub("_0", "", names(odeini))
 
-    res <- suppressWarnings(do.call("mkinfit", mkinfit_call))
-    return(res)
+    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]))
   })
 
-  # Set dimensions with names and the class (mmkin)
-  attributes(mmkin_nlme) <- attributes(x$mmkin_orig[, i])
-
-  plot(mmkin_nlme, main = main, legends = legends,
-    resplot = resplot, standardized = standardized,
-    show_errmin = show_errmin,
-    errmin_var = errmin_var, errmin_digits = errmin_digits,
-    cex = cex,
-    rel.height.middle = rel.height.middle,
-    ymax = ymax, ...)
-
+  degparms_all_pop <- c(fixef(x), degparms_fixed)
+
+  odeparms_pop_trans <- degparms_all_pop[odeparms_names]
+  odeparms_pop <- backtransform_odeparms(odeparms_pop_trans,
+    x$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", "", names(odeini_pop))
+
+  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 top row of plots when we have more than one row
+    # Reduce bottom margin by 2.1 - hides x axis legend
+    if (plot_row == 1 & n_plot_rows > 1) {
+      par(mar = c(3.0, 4.1, 4.1, 2.1))
+    }
+
+    # Margins for middle rows of plots, if any
+    if (plot_row > 1 & plot_row < n_plot_rows) {
+      # Reduce top margin by 2 after the first plot as we have no main title,
+      # reduced plot height, therefore we need rel.height.middle in the layout
+      par(mar = c(3.0, 4.1, 2.1, 2.1))
+    }
+
+    # Margins for bottom row of plots when we have more than one row
+    if (plot_row == n_plot_rows & n_plot_rows > 1) {
+      # Restore bottom margin for last plot to show x axis legend
+      par(mar = c(5.1, 4.1, 2.1, 2.1))
+    }
+
+    plot(pred_pop$time, pred_pop[[obs_var]],
+      main = obs_var,
+      type = "l", lwd = 2,
+      xlim = xlim, ylim = ylim_row,
+      xlab = xlab, ylab = ylab, frame = frame,
+      cex = cex)
+
+    for (ds_i in seq_along(i)) {
+      points(subset(observed_row, ds == ds_names[ds_i], c("time", "value")),
+        col = col_ds[ds_i], pch = pch_ds[ds_i])
+      lines(subset(pred_ds, ds == ds_names[ds_i], c("time", obs_var)),
+        col = col_ds[ds_i], lty = lty_ds[ds_i])
+    }
+
+    if (plot_row %in% legends) {
+      legend(lpos, inset = inset,
+        legend = c("Population mean", ds_names[i]),
+        lty = c(1, lty_ds), lwd = c(2, rep(1, length(i))),
+        col = c(1, col_ds),
+        pch = c(NA, pch_ds))
+    }
+
+    if (identical(maxabs, "auto")) {
+      maxabs = max(abs(observed_row$residual), na.rm = TRUE)
+    }
+
+
+    if (identical(resplot, "time")) {
+      plot(0, type = "n", xlim = xlim, xlab = "Time",
+        main = obs_var,
+        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",
+        main = obs_var,
+        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")
+
+      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 74abeeba..a73b8b09 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -37,6 +37,7 @@ reference:
       - "`[.mmkin`"
       - plot.mmkin
       - AIC.mmkin
+      - print.mmkin
   - title: Mixed models
     desc: Create and work with nonlinear mixed models
     contents:
@@ -44,6 +45,7 @@ reference:
       - plot.nlme.mmkin
       - nlme_function
       - get_deg_func
+      - saemix_model
   - title: Datasets and known results
     contents:
       - FOCUS_2006_A
diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 190bfe87..c29e413d 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -146,7 +146,9 @@
 <a href="#mkin-0-9-50-4-unreleased" class="anchor"></a>mkin 0.9.50.4 (unreleased)<small> Unreleased </small>
 </h1>
 <ul>
-<li>‘saemix_model’, ‘saemix_data’: Helper functions to fit nonlinear mixed-effects models for mmkin row objects using the saemix package</li>
+<li><p>‘plot’ method for ‘nlme.mmkin’ objects</p></li>
+<li><p>‘print’ method for ‘mmkin’ objects</p></li>
+<li><p>‘saemix_model’, ‘saemix_data’: Helper functions to fit nonlinear mixed-effects models for mmkin row objects using the saemix package</p></li>
 </ul>
 </div>
     <div id="mkin-0-9-50-3-2020-10-08" class="section level1">
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index 4bca36e6..8c97cd7c 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: 2020-10-22T11:16Z
+last_built: 2020-10-23T22:30Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/Extract.mmkin.html b/docs/dev/reference/Extract.mmkin.html
index c69259b6..0c02355f 100644
--- a/docs/dev/reference/Extract.mmkin.html
+++ b/docs/dev/reference/Extract.mmkin.html
@@ -40,7 +40,7 @@
 
 
 <meta property="og:title" content="Subsetting method for mmkin objects — [.mmkin" />
-<meta property="og:description" content="Subsetting method for mmkin objects." />
+<meta property="og:description" content="Subsetting method for mmkin objects" />
 
 
 <meta name="robots" content="noindex">
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -120,7 +120,7 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -139,12 +139,12 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Subsetting method for mmkin objects</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mmkin.R'><code>R/mmkin.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mmkin.R'><code>R/mmkin.R</code></a></small>
     <div class="hidden name"><code>Extract.mmkin.Rd</code></div>
     </div>
 
     <div class="ref-description">
-    <p>Subsetting method for mmkin objects.</p>
+    <p>Subsetting method for mmkin objects</p>
     </div>
 
     <pre class="usage"># S3 method for mmkin
@@ -179,30 +179,46 @@ either a list of mkinfit objects or a single mkinfit object.</p></td>
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>An object of class <code><a href='mmkin.html'>mmkin</a></code>.</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='co'># Only use one core, to pass R CMD check --as-cran</span>
-  <span class='no'>fits</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>), <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>B</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>),
-                <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-  <span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#&gt;       dataset
-#&gt; model  B       C      
-#&gt;   FOMC List,39 List,39
-#&gt; attr(,"class")
-#&gt; [1] "mmkin"</div><div class='input'>  <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#&gt;       dataset
-#&gt; model  B      
-#&gt;   SFO  List,39
-#&gt;   FOMC List,39
-#&gt; attr(,"class")
-#&gt; [1] "mmkin"</div><div class='input'>  <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#&gt;      dataset
-#&gt; model B      
-#&gt;   SFO List,39
-#&gt; attr(,"class")
-#&gt; [1] "mmkin"</div><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(
+  <span class='va'>fits</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='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>B <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, C <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>,
+                cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+  <span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span>
+</div><div class='output co'>#&gt; &lt;mmkin&gt; object
+#&gt; Status of individual fits:
+#&gt; 
+#&gt;       dataset
+#&gt; model  B  C 
+#&gt;   FOMC OK OK
+#&gt; 
+#&gt; OK: No warnings</div><div class='input'>  <span class='va'>fits</span><span class='op'>[</span>, <span class='st'>"B"</span><span class='op'>]</span>
+</div><div class='output co'>#&gt; &lt;mmkin&gt; object
+#&gt; Status of individual fits:
+#&gt; 
+#&gt;       dataset
+#&gt; model  B 
+#&gt;   SFO  OK
+#&gt;   FOMC OK
+#&gt; 
+#&gt; OK: No warnings</div><div class='input'>  <span class='va'>fits</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='st'>"B"</span><span class='op'>]</span>
+</div><div class='output co'>#&gt; &lt;mmkin&gt; object
+#&gt; Status of individual fits:
+#&gt; 
+#&gt;      dataset
+#&gt; model B 
+#&gt;   SFO OK
+#&gt; 
+#&gt; OK: No warnings</div><div class='input'>
+  <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span><span class='op'>(</span>
     <span class='co'># This extracts an mkinfit object with lots of components</span>
-    <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span>]]
-  )</div><div class='output co'>#&gt; $par
+    <span class='va'>fits</span><span class='op'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span><span class='op'>]</span><span class='op'>]</span>
+  <span class='op'>)</span>
+</div><div class='output co'>#&gt; $par
 #&gt;  parent_0 log_alpha  log_beta     sigma 
 #&gt; 99.666193  2.549849  5.050586  1.890202 
 #&gt; 
@@ -217,12 +233,11 @@ either a list of mkinfit objects or a single mkinfit object.</p></td>
 #&gt; 
 #&gt; $evaluations
 #&gt; function gradient 
-#&gt;       25       72 
+#&gt;       25       78 
 #&gt; 
 #&gt; $message
 #&gt; [1] "both X-convergence and relative convergence (5)"
-#&gt; </div><div class='input'>
-</div></pre>
+#&gt; </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -238,7 +253,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index 9c8f80fc..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 1b15782a..71c768bd 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 5d70a450..24056025 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -297,6 +297,12 @@ of an mmkin object</p></td>
           <p><code><a href="AIC.mmkin.html">AIC(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i>&lt;mmkin&gt;</i>)</a></code> </p>
         </td>
         <td><p>Calculate the AIC for a column of an mmkin object</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="print.mmkin.html">print(<i>&lt;mmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Print method for mmkin objects</p></td>
       </tr>
     </tbody><tbody>
       <tr>
@@ -334,6 +340,12 @@ of an mmkin object</p></td>
           <p><code><a href="get_deg_func.html">get_deg_func()</a></code> </p>
         </td>
         <td><p>Retrieve a degradation function from the mmkin namespace</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="saemix.html">saemix_model()</a></code> <code><a href="saemix.html">saemix_data()</a></code> </p>
+        </td>
+        <td><p>Create saemix models from mmkin row objects</p></td>
       </tr>
     </tbody><tbody>
       <tr>
diff --git a/docs/dev/reference/plot.nlme.mmkin-1.png b/docs/dev/reference/plot.nlme.mmkin-1.png
index fe2ef7d3..91e3ca52 100644
--- a/docs/dev/reference/plot.nlme.mmkin-1.png
+++ b/docs/dev/reference/plot.nlme.mmkin-1.png
diff --git a/docs/dev/reference/plot.nlme.mmkin-2.png b/docs/dev/reference/plot.nlme.mmkin-2.png
index 265fd2e0..57128ade 100644
--- a/docs/dev/reference/plot.nlme.mmkin-2.png
+++ b/docs/dev/reference/plot.nlme.mmkin-2.png
diff --git a/docs/dev/reference/plot.nlme.mmkin.html b/docs/dev/reference/plot.nlme.mmkin.html
index 7e6124a1..f17a23e3 100644
--- a/docs/dev/reference/plot.nlme.mmkin.html
+++ b/docs/dev/reference/plot.nlme.mmkin.html
@@ -72,7 +72,7 @@
       </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">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -120,7 +120,7 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -139,7 +139,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Plot a fitted nonlinear mixed model obtained via an mmkin row object</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/plot.nlme.mmkin.R'><code>R/plot.nlme.mmkin.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.nlme.mmkin.R'><code>R/plot.nlme.mmkin.R</code></a></small>
     <div class="hidden name"><code>plot.nlme.mmkin.Rd</code></div>
     </div>
 
@@ -148,21 +148,29 @@
     </div>
 
     <pre class="usage"><span class='co'># S3 method for nlme.mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(
-  <span class='no'>x</span>,
-  <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span>(<span class='no'>x</span>$<span class='no'>mmkin_orig</span>),
-  <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
-  <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>,
-  <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"time"</span>, <span class='st'>"errmod"</span>),
-  <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>errmin_var</span> <span class='kw'>=</span> <span class='st'>"All data"</span>,
-  <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>,
-  <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>,
-  <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>,
-  <span class='kw'>ymax</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
-  <span class='no'>...</span>
-)</pre>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
+  <span class='va'>x</span>,
+  i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin_orig</span><span class='op'>)</span>,
+  main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin_orig</span><span class='op'>)</span>,
+  obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
+  standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
+  ylab <span class='op'>=</span> <span class='st'>"Observed"</span>,
+  xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>,
+  legends <span class='op'>=</span> <span class='fl'>1</span>,
+  lpos <span class='op'>=</span> <span class='st'>"topright"</span>,
+  inset <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='fl'>0.05</span>, <span class='fl'>0.05</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>,
+  cex <span class='op'>=</span> <span class='fl'>0.7</span>,
+  rel.height.middle <span class='op'>=</span> <span class='fl'>0.9</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">
@@ -181,35 +189,55 @@ in case plots get too large</p></td>
       <td><p>The main title placed on the outer margin of the plot.</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>ylab</th>
+      <td><p>Label for the y axis.</p></td>
+    </tr>
+    <tr>
+      <th>xlim</th>
+      <td><p>Plot range in x direction.</p></td>
+    </tr>
+    <tr>
       <th>legends</th>
       <td><p>An index for the fits for which legends should be shown.</p></td>
     </tr>
     <tr>
-      <th>resplot</th>
-      <td><p>Should the residuals plotted against time, using
-<code><a href='mkinresplot.html'>mkinresplot</a></code>, or as squared residuals against predicted
-values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td>
+      <th>lpos</th>
+      <td><p>Position(s) of the legend(s). Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> as
+the first argument.  If not length one, this should be of the same length
+as the obs_var argument.</p></td>
     </tr>
     <tr>
-      <th>standardized</th>
-      <td><p>Should the residuals be standardized? This option
-is passed to <code><a href='mkinresplot.html'>mkinresplot</a></code>, it only takes effect if
-<code>resplot = "time"</code>.</p></td>
+      <th>inset</th>
+      <td><p>Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> if applicable.</p></td>
     </tr>
     <tr>
-      <th>show_errmin</th>
-      <td><p>Should the chi2 error level be shown on top of the plots
-to the left?</p></td>
+      <th>resplot</th>
+      <td><p>Should the residuals plotted against time or against
+predicted values?</p></td>
     </tr>
     <tr>
-      <th>errmin_var</th>
-      <td><p>The variable for which the FOCUS chi2 error value should
-be shown.</p></td>
+      <th>ymax</th>
+      <td><p>Vector of maximum y axis values</p></td>
     </tr>
     <tr>
-      <th>errmin_digits</th>
-      <td><p>The number of significant digits for rounding the FOCUS
-chi2 error percentage.</p></td>
+      <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>cex</th>
@@ -221,8 +249,21 @@ chi2 error percentage.</p></td>
 than two rows of plots are shown.</p></td>
     </tr>
     <tr>
-      <th>ymax</th>
-      <td><p>Maximum y axis value for <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p></td>
+      <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>
@@ -234,16 +275,24 @@ than two rows of plots are shown.</p></td>
     <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='no'>ds</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>],
- <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)], <span class='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>))
-<span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='st'>"SFO"</span>, <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.0195</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.011</span></div><div class='input'><span class='co'>#plot(f) # too many panels for pkgdown</span>
-<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f</span>[, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='plot.nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>)
-<span class='no'>f_nlme</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>)
-
-<span class='co'>#plot(f_nlme) # too many panels for pkgdown</span>
-<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='plot.nlme.mmkin-2.png' alt='' width='700' height='433' /></div></pre>
+    <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='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>, cores <span class='op'>=</span> <span class='fl'>1</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.nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span>
+<span class='co'># For this fit we need to increase pnlsMaxiter, and we increase the</span>
+<span class='co'># tolerance in order to speed up the fit for this example evaluation</span>
+<span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-4</span><span class='op'>)</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_nlme</span><span class='op'>)</span>
+</div><div class='img'><img src='plot.nlme.mmkin-2.png' alt='' width='700' height='433' /></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -259,7 +308,7 @@ than two rows of plots are shown.</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/print.mmkin.html b/docs/dev/reference/print.mmkin.html
new file mode 100644
index 00000000..12c67d86
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+++ b/docs/dev/reference/print.mmkin.html
@@ -0,0 +1,194 @@
+<!-- Generated by pkgdown: do not edit by hand -->
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+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
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+      <a href="../articles/mkin.html">Introduction to mkin</a>
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+      <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>
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+</li>
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+    <span class="fab fa fab fa-github fa-lg"></span>
+     
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+</li>
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+      
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+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header>
+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Print method for mmkin objects</h1>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mmkin.R'><code>R/mmkin.R</code></a></small>
+    <div class="hidden name"><code>print.mmkin.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Print method for mmkin objects</p>
+    </div>
+
+    <pre class="usage"><span class='co'># S3 method for 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></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 <a href='mmkin.html'>mmkin</a> object.</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>Not used.</p></td>
+    </tr>
+    </table>
+
+
+  </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 e284abf6..8c4d8cbe 100644
--- a/docs/dev/sitemap.xml
+++ b/docs/dev/sitemap.xml
@@ -166,6 +166,9 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/print.mkinmod.html</loc>
   </url>
   <url>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/print.mmkin.html</loc>
+  </url>
+  <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/reexports.html</loc>
   </url>
   <url>
diff --git a/man/Extract.mmkin.Rd b/man/Extract.mmkin.Rd
index 7677bdba..fd54755c 100644
--- a/man/Extract.mmkin.Rd
+++ b/man/Extract.mmkin.Rd
@@ -22,7 +22,7 @@ either a list of mkinfit objects or a single mkinfit object.}
 An object of class \code{\link{mmkin}}.
 }
 \description{
-Subsetting method for mmkin objects.
+Subsetting method for mmkin objects
 }
 \examples{
 
@@ -37,7 +37,6 @@ Subsetting method for mmkin objects.
     # This extracts an mkinfit object with lots of components
     fits[["FOMC", "B"]]
   )
-
 }
 \author{
 Johannes Ranke
diff --git a/man/plot.nlme.mmkin.Rd b/man/plot.nlme.mmkin.Rd
index 91130402..d1fde212 100644
--- a/man/plot.nlme.mmkin.Rd
+++ b/man/plot.nlme.mmkin.Rd
@@ -7,16 +7,24 @@
 \method{plot}{nlme.mmkin}(
   x,
   i = 1:ncol(x$mmkin_orig),
-  main = "auto",
+  main = rownames(x$mmkin_orig),
+  obs_vars = names(x$mkinmod$map),
+  standardized = TRUE,
+  xlab = "Time",
+  ylab = "Observed",
+  xlim = range(x$data$time),
   legends = 1,
-  resplot = c("time", "errmod"),
-  standardized = FALSE,
-  show_errmin = TRUE,
-  errmin_var = "All data",
-  errmin_digits = 3,
+  lpos = "topright",
+  inset = c(0.05, 0.05),
+  resplot = c("predicted", "time"),
+  ymax = "auto",
+  maxabs = "auto",
   cex = 0.7,
   rel.height.middle = 0.9,
-  ymax = "auto",
+  pch_ds = 1:length(i),
+  col_ds = pch_ds + 1,
+  lty_ds = col_ds,
+  frame = TRUE,
   ...
 )
 }
@@ -28,31 +36,48 @@ in case plots get too large}
 
 \item{main}{The main title placed on the outer margin of the plot.}
 
+\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{ylab}{Label for the y axis.}
+
+\item{xlim}{Plot range in x direction.}
+
 \item{legends}{An index for the fits for which legends should be shown.}
 
-\item{resplot}{Should the residuals plotted against time, using
-\code{\link{mkinresplot}}, or as squared residuals against predicted
-values, with the error model, using \code{\link{mkinerrplot}}.}
+\item{lpos}{Position(s) of the legend(s). Passed to \code{\link{legend}} as
+the first argument.  If not length one, this should be of the same length
+as the obs_var argument.}
 
-\item{standardized}{Should the residuals be standardized? This option
-is passed to \code{\link{mkinresplot}}, it only takes effect if
-\code{resplot = "time"}.}
+\item{inset}{Passed to \code{\link{legend}} if applicable.}
 
-\item{show_errmin}{Should the chi2 error level be shown on top of the plots
-to the left?}
+\item{resplot}{Should the residuals plotted against time or against
+predicted values?}
 
-\item{errmin_var}{The variable for which the FOCUS chi2 error value should
-be shown.}
+\item{ymax}{Vector of maximum y axis values}
 
-\item{errmin_digits}{The number of significant digits for rounding the FOCUS
-chi2 error percentage.}
+\item{maxabs}{Maximum absolute value of the residuals. This is used for the
+scaling of the y axis and defaults to "auto".}
 
 \item{cex}{Passed to the plot functions and \code{\link{mtext}}.}
 
 \item{rel.height.middle}{The relative height of the middle plot, if more
 than two rows of plots are shown.}
 
-\item{ymax}{Maximum y axis value for \code{\link{plot.mkinfit}}.}
+\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{\dots}{Further arguments passed to \code{\link{plot.mkinfit}} and
 \code{\link{mkinresplot}}.}
@@ -65,15 +90,17 @@ Plot a fitted nonlinear mixed model obtained via an mmkin row object
 }
 \examples{
 ds <- lapply(experimental_data_for_UBA_2019[6:10],
- function(x) subset(x$data[c("name", "time", "value")], name == "parent"))
-f <- mmkin("SFO", ds, quiet = TRUE, cores = 1)
-#plot(f) # too many panels for pkgdown
-plot(f[, 3:4])
+ function(x) x$data[c("name", "time", "value")])
+names(ds) <- paste0("ds ", 6:10)
+dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
+  A1 = mkinsub("SFO"), quiet = TRUE)
+f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, cores = 1)
+plot(f[, 3:4], standardized = TRUE)
 library(nlme)
-f_nlme <- nlme(f)
-
-#plot(f_nlme) # too many panels for pkgdown
-plot(f_nlme, 3:4)
+# For this fit we need to increase pnlsMaxiter, and we increase the
+# tolerance in order to speed up the fit for this example evaluation
+f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-4))
+plot(f_nlme)
 }
 \author{
 Johannes Ranke
diff --git a/man/print.mmkin.Rd b/man/print.mmkin.Rd
new file mode 100644
index 00000000..29abe143
--- /dev/null
+++ b/man/print.mmkin.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mmkin.R
+\name{print.mmkin}
+\alias{print.mmkin}
+\title{Print method for mmkin objects}
+\usage{
+\method{print}{mmkin}(x, ...)
+}
+\arguments{
+\item{x}{An \link{mmkin} object.}
+
+\item{\dots}{Not used.}
+}
+\description{
+Print method for mmkin objects
+}