plot.mkinfit <- function(x, fit = x, xlab = "Time", ylab = "Observed", xlim = range(fit$data$time), ylim = range(fit$data$observed, na.rm = TRUE), col_obs = 1:length(fit$mkinmod$map), pch_obs = col_obs, lty_obs = rep(1, length(fit$mkinmod$map)), add = FALSE, legend = !add, ...) { solution_type = fit$solution_type fixed <- fit$fixed$value names(fixed) <- rownames(fit$fixed) parms.all <- c(fit$parms.all, fixed) ininames <- c( rownames(subset(fit$start, type == "state")), rownames(subset(fit$fixed, type == "state"))) odeini <- parms.all[ininames] names(odeini) <- names(fit$mkinmod$diffs) outtimes <- seq(xlim[1], xlim[2], length.out=100) odenames <- c( rownames(subset(fit$start, type == "deparm")), rownames(subset(fit$fixed, type == "deparm"))) odeparms <- parms.all[odenames] out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, atol = fit$atol, rtol = fit$rtol, ...) # Set up the plot if not to be added to an existing plot if (add == FALSE) { plot(0, type="n", xlim = xlim, ylim = ylim, xlab = xlab, ylab = ylab, ...) } # Plot the data and model output names(col_obs) <- names(pch_obs) <- names(lty_obs) <- names(fit$mkinmod$map) for (obs_var in names(fit$mkinmod$map)) { points(subset(fit$data, variable == obs_var, c(time, observed)), pch = pch_obs[obs_var], col = col_obs[obs_var]) } matlines(out$time, out[-1], col = col_obs, lty = lty_obs) if (legend == TRUE) { legend("topright", inset=c(0.05, 0.05), legend=names(fit$mkinmod$map), col=col_obs, pch=pch_obs, lty=lty_obs) } }