plot.mkinfit <- function(x, fit = x,
xlab = "Time", ylab = "Observed",
xlim = range(fit$data$time), ylim = c(0, max(fit$data$observed, na.rm = TRUE)),
col_obs = 1:length(fit$mkinmod$map),
pch_obs = col_obs, lty_obs = 1,
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)
}
}
