Merge plot methods for nlme.mmkin and saem.mmkin

This avoids code duplication

19 files changed, 694 insertions, 359 deletions

diff --git a/NAMESPACE b/NAMESPACE
index 29462082..e6cbe2a7 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -74,6 +74,7 @@ export(mkinresplot)
 export(mkinsub)
 export(mmkin)
 export(nafta)
+export(nlme)
 export(nlme_data)
 export(nlme_function)
 export(parms)
@@ -99,7 +100,6 @@ 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/nlme.mmkin.R b/R/nlme.mmkin.R
index ca849b85..695c63e9 100644
--- a/R/nlme.mmkin.R
+++ b/R/nlme.mmkin.R
@@ -6,6 +6,9 @@
 # following environment will be in the mkin namespace.
 .nlme_env <- new.env(parent = emptyenv())
 
+#' @export
+nlme::nlme
+
 #' Retrieve a degradation function from the mmkin namespace
 #'
 #' @importFrom utils getFromNamespace
diff --git a/R/plot.nlme.mmkin.R b/R/plot.nlme.mmkin.R
deleted file mode 100644
index 4228b18a..00000000
--- a/R/plot.nlme.mmkin.R
+++ /dev/null
@@ -1,216 +0,0 @@
-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
-#' @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 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) x$data[c("name", "time", "value")])
-#' names(ds) <- paste0("ds ", 6:10)
-#' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
-#'   A1 = mkinsub("SFO"), quiet = TRUE)
-#' \dontrun{
-#' f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE)
-#' plot(f[, 3:4], standardized = TRUE)
-#'
-#' library(nlme)
-#' # For this fit we need to increase pnlsMaxiter, and we increase the
-#' # tolerance in order to speed up the fit for this example evaluation
-#' f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3))
-#' plot(f_nlme)
-#' }
-#' @export
-plot.nlme.mmkin <- function(x, i = 1:ncol(x$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 <- coefficients(x)
-  degparms_optim_names <- names(degparms_optim)
-  degparms_fixed <- fit_1$fixed$value
-  names(degparms_fixed) <- rownames(fit_1$fixed)
-  degparms_all <- cbind(as.matrix(degparms_optim),
-    matrix(rep(degparms_fixed, nrow(degparms_optim)),
-      ncol = length(degparms_fixed),
-      nrow = nrow(degparms_optim), byrow = TRUE))
-  degparms_all_names <- c(degparms_optim_names, names(degparms_fixed))
-  colnames(degparms_all) <- degparms_all_names
-
-  odeini_names <- grep("_0$", degparms_all_names, value = TRUE)
-  odeparms_names <- setdiff(degparms_all_names, odeini_names)
-
-  residual_type = ifelse(standardized, "pearson", "response")
-
-  observed <- cbind(x$data,
-    residual = residuals(x, type = residual_type))
-
-  n_plot_rows = length(obs_vars)
-  n_plots = n_plot_rows * 2
-
-  # Set relative plot heights, so the first plot row is the norm
-  rel.heights <- if (n_plot_rows > 1) {
-    c(rel.height.legend, c(rep(1, n_plot_rows - 1), rel.height.bottom))
-  } else {
-    c(rel.height.legend, 1)
-  }
-
-  layout_matrix = matrix(c(1, 1, 2:(n_plots + 1)),
-    n_plot_rows + 1, 2, byrow = TRUE)
-  layout(layout_matrix, heights = rel.heights)
-
-  par(mar = c(0.1, 2.1, 0.6, 2.1))
-
-  plot(0, type = "n", axes = FALSE, ann = FALSE)
-  legend("center", bty = "n", ncol = ncol.legend,
-    legend = c("Population", ds_names[i]),
-    lty = c(1, lty_ds), lwd = c(2, rep(1, length(i))),
-    col = c(1, col_ds),
-    pch = c(NA, pch_ds))
-
-
-  solution_type = fit_1$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_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$transform_fractions)
-
-  odeini_pop <- degparms_all_pop[odeini_names]
-  names(odeini_pop) <- gsub("_0", "", odeini_names)
-
-  pred_pop <- as.data.frame(
-    mkinpredict(x$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/R/plot.saem.mmkin.R b/R/plot_mixed.R
index ce43fdb6..68404de4 100644
--- a/R/plot.saem.mmkin.R
+++ b/R/plot_mixed.R
@@ -1,9 +1,10 @@
 if(getRversion() >= '2.15.1') utils::globalVariables("ds")
 
-#' Plot an saem fitted nonlinear mixed model obtained via an mmkin row object
+#' Plot predictions from a 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,
+#' @name plot_mixed
+#' @param x An object of class [saem.mmkin] or [nlme.mmkin]
+#' @param i A numeric index to select datasets for which to plot the individual predictions,
 #'   in case plots get too large
 #' @inheritParams plot.mkinfit
 #' @param standardized Should the residuals be standardized? Only takes effect if
@@ -19,8 +20,8 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds")
 #'   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.
+#' @importFrom stats coefficients
+#' @return The functions are called for their side effect.
 #' @author Johannes Ranke
 #' @examples
 #' ds <- lapply(experimental_data_for_UBA_2019[6:10],
@@ -32,9 +33,16 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds")
 #' f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE)
 #' plot(f[, 3:4], standardized = TRUE)
 #'
+#' library(nlme)
+#' # 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-3))
+#' plot(f_nlme)
+#'
 #' f_saem <- saem(f)
 #' plot(f_saem)
 #' }
+#' @rdname plot_mixed
 #' @export
 plot.saem.mmkin <- function(x, i = 1:ncol(x$mmkin),
   obs_vars = names(x$mkinmod$map),
@@ -52,33 +60,106 @@ plot.saem.mmkin <- function(x, i = 1:ncol(x$mmkin),
   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$so)
+  degparms_optim <- saemix::psi(x$so)
   rownames(degparms_optim) <- ds_names
   degparms_optim_names <- setdiff(names(fit_1$par), names(fit_1$errparms))
   colnames(degparms_optim) <- degparms_optim_names
 
+  residual_type = ifelse(standardized, "iwres", "ires")
+
+  residuals <- x$so@results@predictions[[residual_type]]
+
+  degparms_pop <- x$so@results@fixed.effects
+  names(degparms_pop) <- degparms_optim_names
+
+  .plot_mixed(x, i,
+    degparms_optim, degparms_pop, residuals,
+    obs_vars, standardized, xlab, xlim,
+    resplot, ymax, maxabs,
+    ncol.legend, nrow.legend,
+    rel.height.legend, rel.height.bottom,
+    pch_ds, col_ds, lty_ds, frame, ...)
+}
+
+#' @rdname plot_mixed
+#' @export
+plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin),
+  obs_vars = names(x$mkinmod$map),
+  standardized = TRUE,
+  xlab = "Time",
+  xlim = range(x$data$time),
+  resplot = c("predicted", "time"),
+  ymax = "auto", maxabs = "auto",
+  ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
+  nrow.legend = ceiling((length(i) + 1) / ncol.legend),
+  rel.height.legend = 0.03 + 0.08 * nrow.legend,
+  rel.height.bottom = 1.1,
+  pch_ds = 1:length(i),
+  col_ds = pch_ds + 1,
+  lty_ds = col_ds,
+  frame = TRUE, ...)
+{
+  degparms_optim <- coefficients(x)
+  degparms_pop <- nlme::fixef(x)
+
+  residuals <- residuals(x,
+    type = ifelse(standardized, "pearson", "response"))
+
+  .plot_mixed(x, i,
+    degparms_optim, degparms_pop, residuals,
+    obs_vars, standardized, xlab, xlim,
+    resplot, ymax, maxabs,
+    ncol.legend, nrow.legend,
+    rel.height.legend, rel.height.bottom,
+    pch_ds, col_ds, lty_ds, frame, ...)
+}
+
+.plot_mixed <- function(x, i = 1:ncol(x$mmkin),
+  degparms_optim,
+  degparms_pop,
+  residuals,
+  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_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))
+  degparms_all_names <- c(names(degparms_optim), names(degparms_fixed))
   colnames(degparms_all) <- degparms_all_names
 
+  degparms_all_pop <- c(degparms_pop, degparms_fixed)
+
   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]])
+    residual = residuals)
 
   n_plot_rows = length(obs_vars)
   n_plots = n_plot_rows * 2
@@ -103,7 +184,6 @@ plot.saem.mmkin <- function(x, i = 1:ncol(x$mmkin),
     col = c(1, col_ds),
     pch = c(NA, pch_ds))
 
-
   solution_type = fit_1$solution_type
 
   outtimes <- sort(unique(c(x$data$time,
@@ -126,10 +206,6 @@ plot.saem.mmkin <- function(x, i = 1:ncol(x$mmkin),
     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,
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index e14af5e0..4b2b76f7 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: 2020-11-09T13:23Z
+last_built: 2020-11-09T15:29Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png
index cd2014eb..8ada7133 100644
--- a/docs/dev/reference/Rplot002.png
+++ b/docs/dev/reference/Rplot002.png
diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png
index 7514f1a4..cd2014eb 100644
--- a/docs/dev/reference/Rplot003.png
+++ b/docs/dev/reference/Rplot003.png
diff --git a/docs/dev/reference/dot-plot_mixed.html b/docs/dev/reference/dot-plot_mixed.html
new file mode 100644
index 00000000..e359c5ea
--- /dev/null
+++ b/docs/dev/reference/dot-plot_mixed.html
@@ -0,0 +1,203 @@
+<!-- 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>Not intended to be called directly by the user — .plot_mixed • 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>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<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="Not intended to be called directly by the user — .plot_mixed" />
+<meta property="og:description" content="Not intended to be called directly by the user" />
+
+
+<meta name="robots" content="noindex">
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+
+  </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">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </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">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    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>
+  <a href="https://github.com/jranke/mkin/">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
+      
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header>
+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Not intended to be called directly by the user</h1>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot_mixed.R'><code>R/plot_mixed.R</code></a></small>
+    <div class="hidden name"><code>dot-plot_mixed.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Not intended to be called directly by the user</p>
+    </div>
+
+    <pre class="usage"><span class='fu'>.plot_mixed</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'>$</span><span class='va'>mmkin</span><span class='op'>)</span>,
+  <span class='va'>degparms_optim</span>,
+  <span class='va'>degparms_pop</span>,
+  <span class='va'>residuals</span>,
+  obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</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>
+
+
+
+  </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/reference/get_deg_func.html b/docs/dev/reference/get_deg_func.html
index ea0676cc..a266bf5f 100644
--- a/docs/dev/reference/get_deg_func.html
+++ b/docs/dev/reference/get_deg_func.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>Retrieve a degradation function from the mmkin namespace</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a></small>
     <div class="hidden name"><code>get_deg_func.Rd</code></div>
     </div>
 
@@ -147,7 +147,7 @@
     <p>Retrieve a degradation function from the mmkin namespace</p>
     </div>
 
-    <pre class="usage"><span class='fu'>get_deg_func</span>()</pre>
+    <pre class="usage"><span class='fu'>get_deg_func</span><span class='op'>(</span><span class='op'>)</span></pre>
 
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -170,7 +170,7 @@ nlme.mmkin</p>
 </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/index.html b/docs/dev/reference/index.html
index f5621402..5ed2044b 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -325,9 +325,9 @@ of an mmkin object</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="plot.nlme.mmkin.html">plot(<i>&lt;nlme.mmkin&gt;</i>)</a></code> </p>
+          <p><code><a href="plot_mixed.html">plot(<i>&lt;saem.mmkin&gt;</i>)</a></code> <code><a href="plot_mixed.html">plot(<i>&lt;nlme.mmkin&gt;</i>)</a></code> </p>
         </td>
-        <td><p>Plot a fitted nonlinear mixed model obtained via an mmkin row object</p></td>
+        <td><p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p></td>
       </tr><tr>
         
         <td>
@@ -349,12 +349,6 @@ 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_mixed-1.png b/docs/dev/reference/plot_mixed-1.png
new file mode 100644
index 00000000..5cb33214
--- /dev/null
+++ b/docs/dev/reference/plot_mixed-1.png
diff --git a/docs/dev/reference/plot_mixed-2.png b/docs/dev/reference/plot_mixed-2.png
new file mode 100644
index 00000000..c0d67204
--- /dev/null
+++ b/docs/dev/reference/plot_mixed-2.png
diff --git a/docs/dev/reference/plot_mixed-3.png b/docs/dev/reference/plot_mixed-3.png
new file mode 100644
index 00000000..67058e6c
--- /dev/null
+++ b/docs/dev/reference/plot_mixed-3.png
diff --git a/docs/dev/reference/plot_mixed.html b/docs/dev/reference/plot_mixed.html
new file mode 100644
index 00000000..b5b3ba49
--- /dev/null
+++ b/docs/dev/reference/plot_mixed.html
@@ -0,0 +1,336 @@
+<!-- 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 predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot_mixed • 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>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<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 predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot_mixed" />
+<meta property="og:description" content="Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object" />
+
+
+<meta name="robots" content="noindex">
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+
+  </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">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </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">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    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>
+  <a href="https://github.com/jranke/mkin/">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
+      
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header>
+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Plot predictions from a 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_mixed.R'><code>R/plot_mixed.R</code></a></small>
+    <div class="hidden name"><code>plot_mixed.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Plot predictions from a 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>
+
+<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</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 <a href='saem.html'>saem.mmkin</a> or <a href='nlme.mmkin.html'>nlme.mmkin</a></p></td>
+    </tr>
+    <tr>
+      <th>i</th>
+      <td><p>A numeric index to select datasets for which to plot the individual predictions,
+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 functions are called for their 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_mixed-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-3</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_mixed-2.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 16:07:05 2020"
+#&gt; ....
+#&gt;     Minimisation finished
+#&gt; [1] "Mon Nov  9 16:07:14 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_mixed-3.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/reference/reexports.html b/docs/dev/reference/reexports.html
index fe27de4b..f12a2690 100644
--- a/docs/dev/reference/reexports.html
+++ b/docs/dev/reference/reexports.html
@@ -45,6 +45,8 @@ below to see their documentation.
 
   lmtestlrtest
 
+  nlmenlme
+
 " />
 
 
@@ -77,7 +79,7 @@ below to see their documentation.
       </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>
 
@@ -125,7 +127,7 @@ below to see their documentation.
       </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>
@@ -144,16 +146,18 @@ below to see their documentation.
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Objects exported from other packages</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/lrtest.mkinfit.R'><code>R/lrtest.mkinfit.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/lrtest.mkinfit.R'><code>R/lrtest.mkinfit.R</code></a>, <a href='https://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a></small>
     <div class="hidden name"><code>reexports.Rd</code></div>
     </div>
 
     <div class="ref-description">
     <p>These objects are imported from other packages. Follow the links
 below to see their documentation.</p>
-<dl'>
+<dl>
   <dt>lmtest</dt><dd><p><code><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></code></p></dd>
 
+  <dt>nlme</dt><dd><p><code><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></code></p></dd>
+
 </dl>
     </div>
 
@@ -175,7 +179,7 @@ below to see their documentation.</p>
 </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/sitemap.xml b/docs/dev/sitemap.xml
index d6f55550..5cfca07a 100644
--- a/docs/dev/sitemap.xml
+++ b/docs/dev/sitemap.xml
@@ -157,10 +157,7 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/plot.nafta.html</loc>
   </url>
   <url>
-    <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>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/plot_mixed.html</loc>
   </url>
   <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/print.mkinds.html</loc>
diff --git a/man/plot.saem.mmkin.Rd b/man/plot.saem.mmkin.Rd
deleted file mode 100644
index 1f674bd7..00000000
--- a/man/plot.saem.mmkin.Rd
+++ /dev/null
@@ -1,94 +0,0 @@
-% 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
-}
diff --git a/man/plot.nlme.mmkin.Rd b/man/plot_mixed.Rd
index f426f77b..d3cee7c9 100644
--- a/man/plot.nlme.mmkin.Rd
+++ b/man/plot_mixed.Rd
@@ -1,9 +1,32 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot.nlme.mmkin.R
-\name{plot.nlme.mmkin}
+% Please edit documentation in R/plot_mixed.R
+\name{plot_mixed}
+\alias{plot_mixed}
+\alias{plot.saem.mmkin}
 \alias{plot.nlme.mmkin}
-\title{Plot a fitted nonlinear mixed model obtained via an mmkin row object}
+\title{Plot predictions from a 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$time),
+  resplot = c("predicted", "time"),
+  ymax = "auto",
+  maxabs = "auto",
+  ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
+  nrow.legend = ceiling((length(i) + 1)/ncol.legend),
+  rel.height.legend = 0.03 + 0.08 * nrow.legend,
+  rel.height.bottom = 1.1,
+  pch_ds = 1:length(i),
+  col_ds = pch_ds + 1,
+  lty_ds = col_ds,
+  frame = TRUE,
+  ...
+)
+
 \method{plot}{nlme.mmkin}(
   x,
   i = 1:ncol(x$mmkin),
@@ -21,13 +44,14 @@
   pch_ds = 1:length(i),
   col_ds = pch_ds + 1,
   lty_ds = col_ds,
-  frame = TRUE
+  frame = TRUE,
+  ...
 )
 }
 \arguments{
-\item{x}{An object of class \code{\link{nlme.mmkin}}}
+\item{x}{An object of class \link{saem.mmkin} or \link{nlme.mmkin}}
 
-\item{i}{A numeric index to select datasets for which to plot the nlme fit,
+\item{i}{A numeric index to select datasets for which to plot the individual predictions,
 in case plots get too large}
 
 \item{obs_vars}{A character vector of names of the observed variables for
@@ -65,12 +89,14 @@ 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.
+The functions are called for their side effect.
 }
 \description{
-Plot a fitted nonlinear mixed model obtained via an mmkin row object
+Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object
 }
 \examples{
 ds <- lapply(experimental_data_for_UBA_2019[6:10],
@@ -87,6 +113,9 @@ library(nlme)
 # tolerance in order to speed up the fit for this example evaluation
 f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3))
 plot(f_nlme)
+
+f_saem <- saem(f)
+plot(f_saem)
 }
 }
 \author{
diff --git a/man/reexports.Rd b/man/reexports.Rd
index bb77acc5..ccba7567 100644
--- a/man/reexports.Rd
+++ b/man/reexports.Rd
@@ -1,9 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/lrtest.mkinfit.R
+% Please edit documentation in R/lrtest.mkinfit.R, R/nlme.mmkin.R
 \docType{import}
 \name{reexports}
 \alias{reexports}
 \alias{lrtest}
+\alias{nlme}
 \title{Objects exported from other packages}
 \keyword{internal}
 \description{
@@ -12,5 +13,7 @@ below to see their documentation.
 
 \describe{
   \item{lmtest}{\code{\link[lmtest]{lrtest}}}
+
+  \item{nlme}{\code{\link[nlme]{nlme}}}
 }}