diff options
Diffstat (limited to 'R/plot.mkinfit.R')
| -rw-r--r-- | R/plot.mkinfit.R | 32 |
1 files changed, 16 insertions, 16 deletions
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index 00598737..3df6c81c 100644 --- a/R/plot.mkinfit.R +++ b/R/plot.mkinfit.R @@ -20,15 +20,15 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "variable", "obse plot.mkinfit <- function(x, fit = x, obs_vars = names(fit$mkinmod$map), xlab = "Time", ylab = "Observed", - xlim = range(fit$data$time), + xlim = range(fit$data$time), ylim = "default", col_obs = 1:length(obs_vars), - pch_obs = col_obs, + pch_obs = col_obs, lty_obs = rep(1, length(obs_vars)), - add = FALSE, legend = !add, + add = FALSE, legend = !add, show_residuals = FALSE, maxabs = "auto", sep_obs = FALSE, rel.height.middle = 0.9, - lpos = "topright", inset = c(0.05, 0.05), + lpos = "topright", inset = c(0.05, 0.05), show_errmin = FALSE, errmin_digits = 3, ...) { if (add && show_residuals) stop("If adding to an existing plot we can not show residuals") @@ -53,12 +53,12 @@ plot.mkinfit <- function(x, fit = x, rownames(subset(fit$fixed, type == "deparm"))) odeparms <- parms.all[odenames] - out <- try(mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, + out <- try(mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, atol = fit$atol, rtol = fit$rtol), silent = TRUE) if (inherits(out, "try-error")) { - out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, + out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, atol = fit$atol, rtol = fit$rtol, use_compiled = FALSE) } @@ -85,7 +85,7 @@ plot.mkinfit <- function(x, fit = x, # and the middle plots (if n_plot_rows >2) are smaller by rel.height.middle rel.heights <- if (n_plot_rows > 2) c(1, rep(rel.height.middle, n_plot_rows - 2), 1) else rep(1, n_plot_rows) - layout_matrix = matrix(1:n_plots, + layout_matrix = matrix(1:n_plots, n_plot_rows, n_plot_cols, byrow = TRUE) layout(layout_matrix, heights = rel.heights) } else { # else show residuals in the lower third to keep compatibility @@ -104,8 +104,8 @@ plot.mkinfit <- function(x, fit = x, # Set ylim to sensible default, or to the specified value if (ylim[[1]] == "default") { - ylim_row = c(0, max(c(subset(fit$data, variable %in% row_obs_vars)$observed, - subset(fit$data, variable %in% row_obs_vars)$fitted), + ylim_row = c(0, max(c(subset(fit$data, variable %in% row_obs_vars)$observed, + subset(fit$data, variable %in% row_obs_vars)$fitted), na.rm = TRUE)) } else { ylim_row = ylim @@ -115,12 +115,12 @@ plot.mkinfit <- function(x, fit = x, # Margins for top row of plots when we have more than one row # Reduce bottom margin by 2.1 - hides x axis legend if (plot_row == 1 & n_plot_rows > 1) { - par(mar = c(3.0, 4.1, 4.1, 2.1)) + par(mar = c(3.0, 4.1, 4.1, 2.1)) } # Margins for middle rows of plots, if any if (plot_row > 1 & plot_row < n_plot_rows) { - # Reduce top margin by 2 after the first plot as we have no main title, + # Reduce top margin by 2 after the first plot as we have no main title, # reduced plot height, therefore we need rel.height.middle in the layout par(mar = c(3.0, 4.1, 2.1, 2.1)) } @@ -134,14 +134,14 @@ plot.mkinfit <- function(x, fit = x, # Set up the main plot if not to be added to an existing plot if (add == FALSE) { - plot(0, type="n", + plot(0, type="n", xlim = xlim, ylim = ylim_row, xlab = xlab, ylab = ylab, ...) } # Plot the data for (obs_var in row_obs_vars) { - points(subset(fit$data, variable == obs_var, c(time, observed)), + points(subset(fit$data, variable == obs_var, c(time, observed)), pch = pch_obs[obs_var], col = col_obs[obs_var]) } @@ -181,8 +181,8 @@ plot.mkinfit <- function(x, fit = x, residuals <- subset(fit$data, variable %in% row_obs_vars, residual) if (maxabs == "auto") maxabs = max(abs(residuals), na.rm = TRUE) if (!sep_obs) par(mar = c(5, 4, 0, 2) + 0.1) - plot(0, type="n", - xlim = xlim, + plot(0, type="n", + xlim = xlim, ylim = c(-1.2 * maxabs, 1.2 * maxabs), xlab = xlab, ylab = "Residuals") for(obs_var in row_obs_vars){ @@ -197,6 +197,6 @@ plot.mkinfit <- function(x, fit = x, # Convenience function for switching on some features of mkinfit # that have not been made the default to keep compatibility plot_sep <- function(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, ...) { - plot.mkinfit(fit, sep_obs = TRUE, show_residuals = TRUE, + plot.mkinfit(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, ...) } |