From 1718d434efae26de02754c6622c43f4dc9e624b9 Mon Sep 17 00:00:00 2001
From: jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date: Thu, 15 Mar 2012 15:54:14 +0000
Subject: Update kinfit and mkin to the latest version published on BerliOS.

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@17 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
---
 R/mkinplot.R | 83 ++++++++++++++++++++++++++++++++++++++++++++++++------------
 1 file changed, 67 insertions(+), 16 deletions(-)

(limited to 'R/mkinplot.R')

diff --git a/R/mkinplot.R b/R/mkinplot.R
index d2880c0e..d665bc23 100644
--- a/R/mkinplot.R
+++ b/R/mkinplot.R
@@ -1,5 +1,6 @@
-mkinplot <- function(fit, xlab = "Time", ylab = "Observed", xlim = range(fit$data$time), ylim = range(fit$data$observed, na.rm = TRUE), ...)
+mkinplot <- function(fit, xlab = "Time", ylab = "Observed", xlim = range(fit$data$time), ylim = range(fit$data$observed, na.rm = TRUE), legend = TRUE, ...)
 {
+  solution = fit$solution
   fixed <- fit$fixed$value
   names(fixed) <- rownames(fit$fixed)
   parms.all <- c(fit$par, fixed)
@@ -16,12 +17,60 @@ mkinplot <- function(fit, xlab = "Time", ylab = "Observed", xlim = range(fit$dat
     rownames(subset(fit$fixed, type == "deparm")))
   odeparms <- parms.all[odenames]
 
-  # Solve the ode
-  out <- ode(
-    y = odeini,
-    times = outtimes,
-    func = fit$mkindiff, 
-    parms = odeparms)
+  # Solve the system
+  evalparse <- function(string)
+  {
+    eval(parse(text=string), as.list(c(odeparms, odeini)))
+  }
+  if (solution == "analytical") {
+    parent.type = names(fit$map[[1]])[1]  
+    parent.name = names(fit$diffs)[[1]]
+    o <- switch(parent.type,
+      SFO = SFO.solution(outtimes, 
+          evalparse(parent.name),
+          evalparse(paste("k", parent.name, "sink", sep="_"))),
+      FOMC = FOMC.solution(outtimes,
+          evalparse(parent.name),
+          evalparse("alpha"), evalparse("beta")),
+      DFOP = DFOP.solution(outtimes,
+          evalparse(parent.name),
+          evalparse("k1"), evalparse("k2"),
+          evalparse("g")),
+      HS = HS.solution(outtimes,
+          evalparse(parent.name),
+          evalparse("k1"), evalparse("k2"),
+          evalparse("tb")),
+      SFORB = SFORB.solution(outtimes,
+          evalparse(parent.name),
+          evalparse(paste("k", parent.name, "free_bound", sep="_")),
+          evalparse(paste("k", parent.name, "bound_free", sep="_")),
+          evalparse(paste("k", parent.name, "free_sink", sep="_")))
+    )
+    out <- cbind(outtimes, o)
+    dimnames(out) <- list(outtimes, c("time", parent.name))
+  }
+  if (solution == "eigen") {
+    coefmat.num <- matrix(sapply(as.vector(fit$coefmat), evalparse), 
+      nrow = length(odeini))
+    e <- eigen(coefmat.num)
+    c <- solve(e$vectors, odeini)
+    f.out <- function(t) {
+      e$vectors %*% diag(exp(e$values * t), nrow=length(odeini)) %*% c
+    }
+    o <- matrix(mapply(f.out, outtimes), 
+      nrow = length(odeini), ncol = length(outtimes))
+    dimnames(o) <- list(names(odeini), NULL)
+    out <- cbind(time = outtimes, t(o))
+  } 
+  if (solution == "deSolve") {
+    out <- ode(
+      y = odeini,
+      times = outtimes,
+      func = fit$mkindiff, 
+      parms = odeparms,
+      atol = fit$atol
+    )
+  }
     
   # Output transformation for models with unobserved compartments like SFORB
   out_transformed <- data.frame(time = out[,"time"])
@@ -36,14 +85,16 @@ mkinplot <- function(fit, xlab = "Time", ylab = "Observed", xlim = range(fit$dat
   # Plot the data and model output
   plot(0, type="n", 
     xlim = xlim, ylim = ylim,
-      xlab = xlab, ylab = ylab, ...)
-    col_obs <- pch_obs <- 1:length(fit$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$map),
+    xlab = xlab, ylab = ylab, ...)
+  col_obs <- pch_obs <- 1:length(fit$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])
+  if (legend == TRUE) {
+    legend("topright", inset=c(0.05, 0.05), legend=names(fit$map),
       col=col_obs, pch=pch_obs, lty=1:length(pch_obs))
+  }
 }
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