1 files changed, 49 insertions, 0 deletions
diff --git a/R/mkinplot.R b/R/mkinplot.R
new file mode 100644
index 0000000..d2880c0
--- /dev/null
+++ b/R/mkinplot.R
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+mkinplot <- function(fit, xlab = "Time", ylab = "Observed", xlim = range(fit$data$time), ylim = range(fit$data$observed, na.rm = TRUE), ...)
+{
+  fixed <- fit$fixed$value
+  names(fixed) <- rownames(fit$fixed)
+  parms.all <- c(fit$par, fixed)
+  ininames <- c(
+    rownames(subset(fit$start, type == "state")),
+    rownames(subset(fit$fixed, type == "state")))
+  odeini <- parms.all[ininames]
+  names(odeini) <- names(fit$diffs)
+
+  outtimes <- seq(xlim[1], xlim[2], length.out=100)
+
+  odenames <- c(
+    rownames(subset(fit$start, type == "deparm")),
+    rownames(subset(fit$fixed, type == "deparm")))
+  odeparms <- parms.all[odenames]
+
+  # Solve the ode
+  out <- ode(
+    y = odeini,
+    times = outtimes,
+    func = fit$mkindiff, 
+    parms = odeparms)
+    
+  # Output transformation for models with unobserved compartments like SFORB
+  out_transformed <- data.frame(time = out[,"time"])
+  for (var in names(fit$map)) {
+    if(length(fit$map[[var]]) == 1) {
+      out_transformed[var] <- out[, var]
+    } else {
+      out_transformed[var] <- rowSums(out[, fit$map[[var]]])
+    }
+  }    
+
+  # Plot the data and model output
+  plot(0, type="n", 
+    xlim = xlim, ylim = ylim,
+      xlab = xlab, ylab = ylab, ...)
+    col_obs <- pch_obs <- 1:length(fit$map)
+    names(col_obs) <- names(pch_obs) <- names(fit$map)
+    for (obs_var in names(fit$map)) {
+      points(subset(fit$data, variable == obs_var, c(time, observed)), 
+        pch = pch_obs[obs_var], col = col_obs[obs_var])
+    }
+    matlines(out_transformed$time, out_transformed[-1])
+      legend("topright", inset=c(0.05, 0.05), legend=names(fit$map),
+      col=col_obs, pch=pch_obs, lty=1:length(pch_obs))
+}