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| -rw-r--r-- | NAMESPACE | 2 | ||||
| -rw-r--r-- | R/plot.saem.mmkin.R | 218 | ||||
| -rw-r--r-- | _pkgdown.yml | 1 | ||||
| -rw-r--r-- | docs/dev/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/dev/reference/Rplot001.png | bin | 1011 -> 27839 bytes | |||
| -rw-r--r-- | docs/dev/reference/Rplot002.png | bin | 57363 -> 56909 bytes | |||
| -rw-r--r-- | docs/dev/reference/index.html | 6 | ||||
| -rw-r--r-- | docs/dev/reference/plot.nlme.mmkin.html | 10 | ||||
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| -rw-r--r-- | docs/dev/reference/plot.saem.mmkin.html | 308 | ||||
| -rw-r--r-- | docs/dev/sitemap.xml | 3 | ||||
| -rw-r--r-- | man/plot.nlme.mmkin.Rd | 8 | ||||
| -rw-r--r-- | man/plot.saem.mmkin.Rd | 94 |
14 files changed, 637 insertions, 15 deletions
@@ -20,6 +20,7 @@ S3method(plot,mkinfit) S3method(plot,mmkin) S3method(plot,nafta) S3method(plot,nlme.mmkin) +S3method(plot,saem.mmkin) S3method(print,mkinds) S3method(print,mkinmod) S3method(print,mmkin) @@ -98,6 +99,7 @@ importFrom(parallel,mclapply) importFrom(parallel,parLapply) importFrom(pkgbuild,has_compiler) importFrom(purrr,map_dfr) +importFrom(saemix,psi) importFrom(stats,AIC) importFrom(stats,BIC) importFrom(stats,aggregate) diff --git a/R/plot.saem.mmkin.R b/R/plot.saem.mmkin.R new file mode 100644 index 00000000..ce43fdb6 --- /dev/null +++ b/R/plot.saem.mmkin.R @@ -0,0 +1,218 @@ +if(getRversion() >= '2.15.1') utils::globalVariables("ds") + +#' Plot an saem fitted nonlinear mixed model obtained via an mmkin row object +#' +#' @param x An object of class \code{\link{saem.mmkin}} +#' @param i A numeric index to select datasets for which to plot the saem fit, +#' in case plots get too large +#' @inheritParams plot.mkinfit +#' @param standardized Should the residuals be standardized? Only takes effect if +#' `resplot = "time"`. +#' @param rel.height.legend The relative height of the legend shown on top +#' @param rel.height.bottom The relative height of the bottom plot row +#' @param ymax Vector of maximum y axis values +#' @param ncol.legend Number of columns to use in the legend +#' @param nrow.legend Number of rows to use in the legend +#' @param resplot Should the residuals plotted against time or against +#' predicted values? +#' @param col_ds Colors used for plotting the observed data and the +#' corresponding model prediction lines for the different datasets. +#' @param pch_ds Symbols to be used for plotting the data. +#' @param lty_ds Line types to be used for the model predictions. +#' @importFrom saemix psi +#' @return The function is called for its side effect. +#' @author Johannes Ranke +#' @examples +#' ds <- lapply(experimental_data_for_UBA_2019[6:10], +#' function(x) x$data[c("name", "time", "value")]) +#' names(ds) <- paste0("ds ", 6:10) +#' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), +#' A1 = mkinsub("SFO"), quiet = TRUE) +#' \dontrun{ +#' f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE) +#' plot(f[, 3:4], standardized = TRUE) +#' +#' f_saem <- saem(f) +#' plot(f_saem) +#' } +#' @export +plot.saem.mmkin <- function(x, i = 1:ncol(x$mmkin), + obs_vars = names(x$mkinmod$map), + standardized = TRUE, + xlab = "Time", + xlim = range(x$data$time), + resplot = c("predicted", "time"), + ymax = "auto", maxabs = "auto", + ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)), + nrow.legend = ceiling((length(i) + 1) / ncol.legend), + rel.height.legend = 0.03 + 0.08 * nrow.legend, + rel.height.bottom = 1.1, + pch_ds = 1:length(i), + col_ds = pch_ds + 1, + lty_ds = col_ds, + frame = TRUE, ...) +{ + + oldpar <- par(no.readonly = TRUE) + + fit_1 <- x$mmkin[[1]] + ds_names <- colnames(x$mmkin) + + degparms_optim <- psi(x$so) + rownames(degparms_optim) <- ds_names + degparms_optim_names <- setdiff(names(fit_1$par), names(fit_1$errparms)) + colnames(degparms_optim) <- degparms_optim_names + + degparms_fixed <- fit_1$fixed$value + names(degparms_fixed) <- rownames(fit_1$fixed) + degparms_all <- cbind(as.matrix(degparms_optim), + matrix(rep(degparms_fixed, nrow(degparms_optim)), + ncol = length(degparms_fixed), + nrow = nrow(degparms_optim), byrow = TRUE)) + degparms_all_names <- c(degparms_optim_names, names(degparms_fixed)) + colnames(degparms_all) <- degparms_all_names + + odeini_names <- grep("_0$", degparms_all_names, value = TRUE) + odeparms_names <- setdiff(degparms_all_names, odeini_names) + + residual_type = ifelse(standardized, "iwres", "ires") + + observed <- cbind(x$data, + residual = x$so@results@predictions[[residual_type]]) + + n_plot_rows = length(obs_vars) + n_plots = n_plot_rows * 2 + + # Set relative plot heights, so the first plot row is the norm + rel.heights <- if (n_plot_rows > 1) { + c(rel.height.legend, c(rep(1, n_plot_rows - 1), rel.height.bottom)) + } else { + c(rel.height.legend, 1) + } + + layout_matrix = matrix(c(1, 1, 2:(n_plots + 1)), + n_plot_rows + 1, 2, byrow = TRUE) + layout(layout_matrix, heights = rel.heights) + + par(mar = c(0.1, 2.1, 0.6, 2.1)) + + plot(0, type = "n", axes = FALSE, ann = FALSE) + legend("center", bty = "n", ncol = ncol.legend, + legend = c("Population", ds_names[i]), + lty = c(1, lty_ds), lwd = c(2, rep(1, length(i))), + col = c(1, col_ds), + pch = c(NA, pch_ds)) + + + solution_type = fit_1$solution_type + + outtimes <- sort(unique(c(x$data$time, + seq(xlim[1], xlim[2], length.out = 50)))) + + pred_ds <- purrr::map_dfr(i, function(ds_i) { + odeparms_trans <- degparms_all[ds_i, odeparms_names] + names(odeparms_trans) <- odeparms_names # needed if only one odeparm + odeparms <- backtransform_odeparms(odeparms_trans, + x$mkinmod, + transform_rates = fit_1$transform_rates, + transform_fractions = fit_1$transform_fractions) + + odeini <- degparms_all[ds_i, odeini_names] + names(odeini) <- gsub("_0", "", odeini_names) + + out <- mkinpredict(x$mkinmod, odeparms, odeini, + outtimes, solution_type = solution_type, + atol = fit_1$atol, rtol = fit_1$rtol) + return(cbind(as.data.frame(out), ds = ds_names[ds_i])) + }) + + degparms_pop <- x$so@results@fixed.effects + names(degparms_pop) <- degparms_optim_names + degparms_all_pop <- c(degparms_pop, degparms_fixed) + + odeparms_pop_trans <- degparms_all_pop[odeparms_names] + odeparms_pop <- backtransform_odeparms(odeparms_pop_trans, + x$mkinmod, + transform_rates = fit_1$transform_rates, + transform_fractions = fit_1$transform_fractions) + + odeini_pop <- degparms_all_pop[odeini_names] + names(odeini_pop) <- gsub("_0", "", odeini_names) + + pred_pop <- as.data.frame( + mkinpredict(x$mkinmod, odeparms_pop, odeini_pop, + outtimes, solution_type = solution_type, + atol = fit_1$atol, rtol = fit_1$rtol)) + + resplot <- match.arg(resplot) + + # Loop plot rows + for (plot_row in 1:n_plot_rows) { + + obs_var <- obs_vars[plot_row] + observed_row <- subset(observed, name == obs_var) + + # Set ylim to sensible default, or use ymax + if (identical(ymax, "auto")) { + ylim_row = c(0, + max(c(observed_row$value, pred_ds[[obs_var]]), na.rm = TRUE)) + } else { + ylim_row = c(0, ymax[plot_row]) + } + + # Margins for bottom row of plots when we have more than one row + # This is the only row that needs to show the x axis legend + if (plot_row == n_plot_rows) { + par(mar = c(5.1, 4.1, 2.1, 2.1)) + } else { + par(mar = c(3.0, 4.1, 2.1, 2.1)) + } + + plot(pred_pop$time, pred_pop[[obs_var]], + type = "l", lwd = 2, + xlim = xlim, ylim = ylim_row, + xlab = xlab, ylab = obs_var, frame = frame) + + for (ds_i in seq_along(i)) { + points(subset(observed_row, ds == ds_names[ds_i], c("time", "value")), + col = col_ds[ds_i], pch = pch_ds[ds_i]) + lines(subset(pred_ds, ds == ds_names[ds_i], c("time", obs_var)), + col = col_ds[ds_i], lty = lty_ds[ds_i]) + } + + if (identical(maxabs, "auto")) { + maxabs = max(abs(observed_row$residual), na.rm = TRUE) + } + + if (identical(resplot, "time")) { + plot(0, type = "n", xlim = xlim, xlab = "Time", + ylim = c(-1.2 * maxabs, 1.2 * maxabs), + ylab = if (standardized) "Standardized residual" else "Residual") + + abline(h = 0, lty = 2) + + for (ds_i in seq_along(i)) { + points(subset(observed_row, ds == ds_names[ds_i], c("time", "residual")), + col = col_ds[ds_i], pch = pch_ds[ds_i]) + } + } + + if (identical(resplot, "predicted")) { + plot(0, type = "n", + xlim = c(0, max(pred_ds[[obs_var]])), + xlab = "Predicted", + ylim = c(-1.2 * maxabs, 1.2 * maxabs), + ylab = if (standardized) "Standardized residual" else "Residual") + + abline(h = 0, lty = 2) + + for (ds_i in seq_along(i)) { + observed_row_ds <- merge( + subset(observed_row, ds == ds_names[ds_i], c("time", "residual")), + subset(pred_ds, ds == ds_names[ds_i], c("time", obs_var))) + points(observed_row_ds[c(3, 2)], + col = col_ds[ds_i], pch = pch_ds[ds_i]) + } + } + } +} diff --git a/_pkgdown.yml b/_pkgdown.yml index b036ed59..61c69a9d 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -46,6 +46,7 @@ reference: - summary.nlme.mmkin - saem.mmkin - summary.saem.mmkin + - plot.saem.mmkin - nlme_function - get_deg_func - saemix_model diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index a8bb6144..e14af5e0 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2020-11-09T08:23Z +last_built: 2020-11-09T13:23Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex 17a35806..cfc5bc2b 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png Binary files differindex 8ada7133..cd2014eb 100644 --- a/docs/dev/reference/Rplot002.png +++ b/docs/dev/reference/Rplot002.png diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 825c4d27..f5621402 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -349,6 +349,12 @@ of an mmkin object</p></td> </tr><tr> <td> + <p><code><a href="plot.saem.mmkin.html">plot(<i><saem.mmkin></i>)</a></code> </p> + </td> + <td><p>Plot an saem fitted nonlinear mixed model obtained via an mmkin row object</p></td> + </tr><tr> + + <td> <p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">mean_degparms()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p> </td> <td><p>Helper functions to create nlme models from mmkin row objects</p></td> diff --git a/docs/dev/reference/plot.nlme.mmkin.html b/docs/dev/reference/plot.nlme.mmkin.html index 267bef05..8f5f85f7 100644 --- a/docs/dev/reference/plot.nlme.mmkin.html +++ b/docs/dev/reference/plot.nlme.mmkin.html @@ -150,7 +150,7 @@ <pre class="usage"><span class='co'># S3 method for nlme.mmkin</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span> <span class='va'>x</span>, - i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin_orig</span><span class='op'>)</span>, + i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>, obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span>, xlab <span class='op'>=</span> <span class='st'>"Time"</span>, @@ -165,8 +165,7 @@ pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>, col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>, lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>, - frame <span class='op'>=</span> <span class='cn'>TRUE</span>, - <span class='va'>...</span> + frame <span class='op'>=</span> <span class='cn'>TRUE</span> <span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> @@ -247,11 +246,6 @@ corresponding model prediction lines for the different datasets.</p></td> <th>frame</th> <td><p>Should a frame be drawn around the plots?</p></td> </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and -<code><a href='mkinresplot.html'>mkinresplot</a></code>.</p></td> - </tr> </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> diff --git a/docs/dev/reference/plot.saem.mmkin-1.png b/docs/dev/reference/plot.saem.mmkin-1.png Binary files differnew file mode 100644 index 00000000..5cb33214 --- /dev/null +++ b/docs/dev/reference/plot.saem.mmkin-1.png diff --git a/docs/dev/reference/plot.saem.mmkin-2.png b/docs/dev/reference/plot.saem.mmkin-2.png Binary files differnew file mode 100644 index 00000000..67058e6c --- /dev/null +++ b/docs/dev/reference/plot.saem.mmkin-2.png diff --git a/docs/dev/reference/plot.saem.mmkin.html b/docs/dev/reference/plot.saem.mmkin.html new file mode 100644 index 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class="hidden name"><code>plot.saem.mmkin.Rd</code></div> + </div> + + <div class="ref-description"> + <p>Plot an saem fitted nonlinear mixed model obtained via an mmkin row object</p> + </div> + + <pre class="usage"><span class='co'># S3 method for saem.mmkin</span> +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span> + <span class='va'>x</span>, + i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>, + obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>, + standardized <span class='op'>=</span> <span class='cn'>TRUE</span>, + xlab <span class='op'>=</span> <span class='st'>"Time"</span>, + xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>, + resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>, + ymax <span class='op'>=</span> <span class='st'>"auto"</span>, + maxabs <span class='op'>=</span> <span class='st'>"auto"</span>, + ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'><=</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'><=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>, + nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>, + rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>, + rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>, + pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>, + col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>, + lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>, + frame <span class='op'>=</span> <span class='cn'>TRUE</span>, + <span class='va'>...</span> +<span class='op'>)</span></pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>x</th> + <td><p>An object of class <code><a href='saem.html'>saem.mmkin</a></code></p></td> + </tr> + <tr> + <th>i</th> + <td><p>A numeric index to select datasets for which to plot the saem fit, +in case plots get too large</p></td> + </tr> + <tr> + <th>obs_vars</th> + <td><p>A character vector of names of the observed variables for +which the data and the model should be plotted. Defauls to all observed +variables in the model.</p></td> + </tr> + <tr> + <th>standardized</th> + <td><p>Should the residuals be standardized? Only takes effect if +<code>resplot = "time"</code>.</p></td> + </tr> + <tr> + <th>xlab</th> + <td><p>Label for the x axis.</p></td> + </tr> + <tr> + <th>xlim</th> + <td><p>Plot range in x direction.</p></td> + </tr> + <tr> + <th>resplot</th> + <td><p>Should the residuals plotted against time or against +predicted values?</p></td> + </tr> + <tr> + <th>ymax</th> + <td><p>Vector of maximum y axis values</p></td> + </tr> + <tr> + <th>maxabs</th> + <td><p>Maximum absolute value of the residuals. This is used for the +scaling of the y axis and defaults to "auto".</p></td> + </tr> + <tr> + <th>ncol.legend</th> + <td><p>Number of columns to use in the legend</p></td> + </tr> + <tr> + <th>nrow.legend</th> + <td><p>Number of rows to use in the legend</p></td> + </tr> + <tr> + <th>rel.height.legend</th> + <td><p>The relative height of the legend shown on top</p></td> + </tr> + <tr> + <th>rel.height.bottom</th> + <td><p>The relative height of the bottom plot row</p></td> + </tr> + <tr> + <th>pch_ds</th> + <td><p>Symbols to be used for plotting the data.</p></td> + </tr> + <tr> + <th>col_ds</th> + <td><p>Colors used for plotting the observed data and the +corresponding model prediction lines for the different datasets.</p></td> + </tr> + <tr> + <th>lty_ds</th> + <td><p>Line types to be used for the model predictions.</p></td> + </tr> + <tr> + <th>frame</th> + <td><p>Should a frame be drawn around the plots?</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The function is called for its side effect.</p> + <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + + <p>Johannes Ranke</p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'><-</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'><-</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'><-</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'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='img'><img src='plot.saem.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='va'>f_saem</span> <span class='op'><-</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'>#> Running main SAEM algorithm +#> [1] "Mon Nov 9 14:21:22 2020" +#> .... +#> Minimisation finished +#> [1] "Mon Nov 9 14:21:31 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span> +</div><div class='img'><img src='plot.saem.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> +</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml index d9ef2228..d6f55550 100644 --- a/docs/dev/sitemap.xml +++ b/docs/dev/sitemap.xml @@ -160,6 +160,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/plot.nlme.mmkin.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/plot.saem.mmkin.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/print.mkinds.html</loc> </url> <url> diff --git a/man/plot.nlme.mmkin.Rd b/man/plot.nlme.mmkin.Rd index 5f0f0ef1..f426f77b 100644 --- a/man/plot.nlme.mmkin.Rd +++ b/man/plot.nlme.mmkin.Rd @@ -6,7 +6,7 @@ \usage{ \method{plot}{nlme.mmkin}( x, - i = 1:ncol(x$mmkin_orig), + i = 1:ncol(x$mmkin), obs_vars = names(x$mkinmod$map), standardized = TRUE, xlab = "Time", @@ -21,8 +21,7 @@ pch_ds = 1:length(i), col_ds = pch_ds + 1, lty_ds = col_ds, - frame = TRUE, - ... + frame = TRUE ) } \arguments{ @@ -66,9 +65,6 @@ corresponding model prediction lines for the different datasets.} \item{lty_ds}{Line types to be used for the model predictions.} \item{frame}{Should a frame be drawn around the plots?} - -\item{\dots}{Further arguments passed to \code{\link{plot.mkinfit}} and -\code{\link{mkinresplot}}.} } \value{ The function is called for its side effect. diff --git a/man/plot.saem.mmkin.Rd b/man/plot.saem.mmkin.Rd new file mode 100644 index 00000000..1f674bd7 --- /dev/null +++ b/man/plot.saem.mmkin.Rd @@ -0,0 +1,94 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/plot.saem.mmkin.R +\name{plot.saem.mmkin} +\alias{plot.saem.mmkin} +\title{Plot an saem fitted nonlinear mixed model obtained via an mmkin row object} +\usage{ +\method{plot}{saem.mmkin}( + x, + i = 1:ncol(x$mmkin), + obs_vars = names(x$mkinmod$map), + standardized = TRUE, + xlab = "Time", + xlim = range(x$data$time), + resplot = c("predicted", "time"), + ymax = "auto", + maxabs = "auto", + ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)), + nrow.legend = ceiling((length(i) + 1)/ncol.legend), + rel.height.legend = 0.03 + 0.08 * nrow.legend, + rel.height.bottom = 1.1, + pch_ds = 1:length(i), + col_ds = pch_ds + 1, + lty_ds = col_ds, + frame = TRUE, + ... +) +} +\arguments{ +\item{x}{An object of class \code{\link{saem.mmkin}}} + +\item{i}{A numeric index to select datasets for which to plot the saem fit, +in case plots get too large} + +\item{obs_vars}{A character vector of names of the observed variables for +which the data and the model should be plotted. Defauls to all observed +variables in the model.} + +\item{standardized}{Should the residuals be standardized? Only takes effect if +\code{resplot = "time"}.} + +\item{xlab}{Label for the x axis.} + +\item{xlim}{Plot range in x direction.} + +\item{resplot}{Should the residuals plotted against time or against +predicted values?} + +\item{ymax}{Vector of maximum y axis values} + +\item{maxabs}{Maximum absolute value of the residuals. This is used for the +scaling of the y axis and defaults to "auto".} + +\item{ncol.legend}{Number of columns to use in the legend} + +\item{nrow.legend}{Number of rows to use in the legend} + +\item{rel.height.legend}{The relative height of the legend shown on top} + +\item{rel.height.bottom}{The relative height of the bottom plot row} + +\item{pch_ds}{Symbols to be used for plotting the data.} + +\item{col_ds}{Colors used for plotting the observed data and the +corresponding model prediction lines for the different datasets.} + +\item{lty_ds}{Line types to be used for the model predictions.} + +\item{frame}{Should a frame be drawn around the plots?} + +\item{...}{Further arguments passed to \code{\link{plot}}.} +} +\value{ +The function is called for its side effect. +} +\description{ +Plot an saem fitted nonlinear mixed model obtained via an mmkin row object +} +\examples{ +ds <- lapply(experimental_data_for_UBA_2019[6:10], + function(x) x$data[c("name", "time", "value")]) +names(ds) <- paste0("ds ", 6:10) +dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), + A1 = mkinsub("SFO"), quiet = TRUE) +\dontrun{ +f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE) +plot(f[, 3:4], standardized = TRUE) + +f_saem <- saem(f) +plot(f_saem) +} +} +\author{ +Johannes Ranke +} |
