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-rw-r--r--NAMESPACE2
-rw-r--r--R/nlme.mmkin.R3
-rw-r--r--R/plot.nlme.mmkin.R216
-rw-r--r--R/plot_mixed.R (renamed from R/plot.saem.mmkin.R)108
-rw-r--r--docs/dev/pkgdown.yml2
-rw-r--r--docs/dev/reference/Rplot002.pngbin56909 -> 57363 bytes
-rw-r--r--docs/dev/reference/Rplot003.pngbin52903 -> 56909 bytes
-rw-r--r--docs/dev/reference/dot-plot_mixed.html203
-rw-r--r--docs/dev/reference/get_deg_func.html10
-rw-r--r--docs/dev/reference/index.html10
-rw-r--r--docs/dev/reference/plot_mixed-1.pngbin0 -> 86076 bytes
-rw-r--r--docs/dev/reference/plot_mixed-2.pngbin0 -> 164488 bytes
-rw-r--r--docs/dev/reference/plot_mixed-3.pngbin0 -> 164014 bytes
-rw-r--r--docs/dev/reference/plot_mixed.html336
-rw-r--r--docs/dev/reference/reexports.html14
-rw-r--r--docs/dev/sitemap.xml5
-rw-r--r--man/plot.saem.mmkin.Rd94
-rw-r--r--man/plot_mixed.Rd (renamed from man/plot.nlme.mmkin.Rd)45
-rw-r--r--man/reexports.Rd5
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
Binary files differ
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
Binary files differ
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>
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+ <body data-spy="scroll" data-target="#toc">
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">mkin</a>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ </span>
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+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Functions and data</a>
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+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/mkin.html">Introduction to mkin</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ <li>
+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+ <li>
+ <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
Binary files differ
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
Binary files differ
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
Binary files differ
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">
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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+<script src="../bootstrap-toc.js"></script>
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
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+<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}}}
}}

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