diff options
| -rw-r--r-- | R/plot.nlme.mmkin.R | 46 | ||||
| -rw-r--r-- | docs/dev/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/dev/reference/Rplot002.png | bin | 63682 -> 64132 bytes | |||
| -rw-r--r-- | docs/dev/reference/plot.nlme.mmkin-2.png | bin | 177237 -> 179274 bytes | |||
| -rw-r--r-- | docs/dev/reference/plot.nlme.mmkin.html | 21 | ||||
| -rw-r--r-- | man/plot.nlme.mmkin.Rd | 15 |
6 files changed, 23 insertions, 61 deletions
diff --git a/R/plot.nlme.mmkin.R b/R/plot.nlme.mmkin.R index 084099ac..2356070e 100644 --- a/R/plot.nlme.mmkin.R +++ b/R/plot.nlme.mmkin.R @@ -10,9 +10,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds") #' @param legends An index for the fits for which legends should be shown. #' @param standardized Should the residuals be standardized? Only takes effect if #' `resplot = "time"`. -#' @param cex Passed to the plot functions and \code{\link{mtext}}. -#' @param rel.height.middle The relative height of the middle plot, if more -#' than two rows of plots are shown. +#' @param rel.height.bottom The relative height of the bottom plot row #' @param ymax Vector of maximum y axis values #' @param \dots Further arguments passed to \code{\link{plot.mkinfit}} and #' \code{\link{mkinresplot}}. @@ -36,20 +34,20 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds") #' 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-4)) +#' f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3)) #' plot(f_nlme) #' @export plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), - main = rownames(x$mmkin_orig), + main = NULL, obs_vars = names(x$mkinmod$map), standardized = TRUE, - xlab = "Time", ylab = "Observed", + xlab = "Time", xlim = range(x$data$time), legends = 1, lpos = "topright", inset = c(0.05, 0.05), resplot = c("predicted", "time"), ymax = "auto", maxabs = "auto", - cex = 0.7, rel.height.middle = 0.9, + rel.height.bottom = 1.1, pch_ds = 1:length(i), col_ds = pch_ds + 1, lty_ds = col_ds, @@ -82,11 +80,7 @@ plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), # Set relative plot heights, so the first and the last plot are the norm # and the middle plots (if n_plot_rows >2) are smaller by rel.height.middle - rel.heights <- if (n_plot_rows > 2) { - c(1, rep(rel.height.middle, n_plot_rows - 2), 1) - } else { - rep(1, n_plot_rows) - } + rel.heights <- if (n_plot_rows > 1) c(rep(1, n_plot_rows - 1), rel.height.bottom) else 1 layout_matrix = matrix(1:n_plots, n_plot_rows, 2, byrow = TRUE) @@ -145,31 +139,18 @@ plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), ylim_row = c(0, ymax[plot_row]) } - # Margins for top row of plots when we have more than one row - # Reduce bottom margin by 2.1 - hides x axis legend - if (plot_row == 1 & n_plot_rows > 1) { - par(mar = c(3.0, 4.1, 4.1, 2.1)) - } - - # Margins for middle rows of plots, if any - if (plot_row > 1 & plot_row < n_plot_rows) { - # Reduce top margin by 2 after the first plot as we have no main title, - # reduced plot height, therefore we need rel.height.middle in the layout - par(mar = c(3.0, 4.1, 2.1, 2.1)) - } - # Margins for bottom row of plots when we have more than one row - if (plot_row == n_plot_rows & n_plot_rows > 1) { - # Restore bottom margin for last plot to show x axis legend + # 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$time, pred_pop[[obs_var]], - main = obs_var, type = "l", lwd = 2, xlim = xlim, ylim = ylim_row, - xlab = xlab, ylab = ylab, frame = frame, - cex = cex) + xlab = xlab, ylab = obs_var, frame = frame) for (ds_i in seq_along(i)) { points(subset(observed_row, ds == ds_names[ds_i], c("time", "value")), @@ -180,7 +161,7 @@ plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), if (plot_row %in% legends) { legend(lpos, inset = inset, - legend = c("Population mean", ds_names[i]), + 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)) @@ -193,9 +174,9 @@ plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), if (identical(resplot, "time")) { plot(0, type = "n", xlim = xlim, xlab = "Time", - main = obs_var, ylim = c(-1.2 * maxabs, 1.2 * maxabs), ylab = if (standardized) "Standardized residual" else "Residual") + abline(h = 0, lty = 2) for (ds_i in seq_along(i)) { @@ -206,7 +187,6 @@ plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), if (identical(resplot, "predicted")) { plot(0, type = "n", - main = obs_var, xlim = c(0, max(pred_ds[[obs_var]])), xlab = "Predicted", ylim = c(-1.2 * maxabs, 1.2 * maxabs), diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 8c97cd7c..61fa6e5d 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2020-10-23T22:30Z +last_built: 2020-10-23T23:38Z 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 Binary files differindex 71c768bd..cffa10c1 100644 --- a/docs/dev/reference/Rplot002.png +++ b/docs/dev/reference/Rplot002.png diff --git a/docs/dev/reference/plot.nlme.mmkin-2.png b/docs/dev/reference/plot.nlme.mmkin-2.png Binary files differindex 57128ade..4ec26146 100644 --- a/docs/dev/reference/plot.nlme.mmkin-2.png +++ b/docs/dev/reference/plot.nlme.mmkin-2.png diff --git a/docs/dev/reference/plot.nlme.mmkin.html b/docs/dev/reference/plot.nlme.mmkin.html index f17a23e3..c633e15a 100644 --- a/docs/dev/reference/plot.nlme.mmkin.html +++ b/docs/dev/reference/plot.nlme.mmkin.html @@ -151,11 +151,10 @@ <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span> <span class='va'>x</span>, i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin_orig</span><span class='op'>)</span>, - main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin_orig</span><span class='op'>)</span>, + main <span class='op'>=</span> <span class='cn'>NULL</span>, obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span>, xlab <span class='op'>=</span> <span class='st'>"Time"</span>, - ylab <span class='op'>=</span> <span class='st'>"Observed"</span>, xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>, legends <span class='op'>=</span> <span class='fl'>1</span>, lpos <span class='op'>=</span> <span class='st'>"topright"</span>, @@ -163,8 +162,7 @@ resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>, ymax <span class='op'>=</span> <span class='st'>"auto"</span>, maxabs <span class='op'>=</span> <span class='st'>"auto"</span>, - cex <span class='op'>=</span> <span class='fl'>0.7</span>, - rel.height.middle <span class='op'>=</span> <span class='fl'>0.9</span>, + 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>, @@ -204,10 +202,6 @@ variables in the model.</p></td> <td><p>Label for the x axis.</p></td> </tr> <tr> - <th>ylab</th> - <td><p>Label for the y axis.</p></td> - </tr> - <tr> <th>xlim</th> <td><p>Plot range in x direction.</p></td> </tr> @@ -240,13 +234,8 @@ predicted values?</p></td> scaling of the y axis and defaults to "auto".</p></td> </tr> <tr> - <th>cex</th> - <td><p>Passed to the plot functions and <code><a href='https://rdrr.io/r/graphics/mtext.html'>mtext</a></code>.</p></td> - </tr> - <tr> - <th>rel.height.middle</th> - <td><p>The relative height of the middle plot, if more -than two rows of plots are shown.</p></td> + <th>rel.height.bottom</th> + <td><p>The relative height of the bottom plot row</p></td> </tr> <tr> <th>pch_ds</th> @@ -290,7 +279,7 @@ corresponding model prediction lines for the different datasets.</p></td> </div><div class='img'><img src='plot.nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span> <span class='co'># For this fit we need to increase pnlsMaxiter, and we increase the</span> <span class='co'># tolerance in order to speed up the fit for this example evaluation</span> -<span class='va'>f_nlme</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-4</span><span class='op'>)</span><span class='op'>)</span> +<span class='va'>f_nlme</span> <span class='op'><-</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.nlme.mmkin-2.png' alt='' width='700' height='433' /></div></pre> </div> diff --git a/man/plot.nlme.mmkin.Rd b/man/plot.nlme.mmkin.Rd index d1fde212..5f6e4ed3 100644 --- a/man/plot.nlme.mmkin.Rd +++ b/man/plot.nlme.mmkin.Rd @@ -7,11 +7,10 @@ \method{plot}{nlme.mmkin}( x, i = 1:ncol(x$mmkin_orig), - main = rownames(x$mmkin_orig), + main = NULL, obs_vars = names(x$mkinmod$map), standardized = TRUE, xlab = "Time", - ylab = "Observed", xlim = range(x$data$time), legends = 1, lpos = "topright", @@ -19,8 +18,7 @@ resplot = c("predicted", "time"), ymax = "auto", maxabs = "auto", - cex = 0.7, - rel.height.middle = 0.9, + rel.height.bottom = 1.1, pch_ds = 1:length(i), col_ds = pch_ds + 1, lty_ds = col_ds, @@ -45,8 +43,6 @@ variables in the model.} \item{xlab}{Label for the x axis.} -\item{ylab}{Label for the y axis.} - \item{xlim}{Plot range in x direction.} \item{legends}{An index for the fits for which legends should be shown.} @@ -65,10 +61,7 @@ predicted values?} \item{maxabs}{Maximum absolute value of the residuals. This is used for the scaling of the y axis and defaults to "auto".} -\item{cex}{Passed to the plot functions and \code{\link{mtext}}.} - -\item{rel.height.middle}{The relative height of the middle plot, if more -than two rows of plots are shown.} +\item{rel.height.bottom}{The relative height of the bottom plot row} \item{pch_ds}{Symbols to be used for plotting the data.} @@ -99,7 +92,7 @@ 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-4)) +f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3)) plot(f_nlme) } \author{ |
