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-rw-r--r--R/plot.nlme.mmkin.R46
1 files changed, 13 insertions, 33 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),

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