1 files changed, 80 insertions, 0 deletions
diff --git a/branches/0.1/chemCal/R/calplot.R b/branches/0.1/chemCal/R/calplot.R
new file mode 100644
index 0000000..6aed9c0
--- /dev/null
+++ b/branches/0.1/chemCal/R/calplot.R
@@ -0,0 +1,80 @@
+calplot <- function(object, 
+  xlim = c("auto", "auto"), ylim = c("auto", "auto"), 
+  xlab = "Concentration", ylab = "Response", alpha = 0.05,
+  varfunc = NULL)
+{
+  UseMethod("calplot")
+}
+
+calplot.default <- function(object, 
+  xlim = c("auto","auto"), ylim = c("auto","auto"), 
+  xlab = "Concentration", ylab = "Response",
+  alpha=0.05, varfunc = NULL)
+{
+  stop("Calibration plots only implemented for univariate lm objects.")
+}
+
+calplot.lm <- function(object,
+  xlim = c("auto","auto"), ylim = c("auto","auto"), 
+  xlab = "Concentration", ylab = "Response", alpha=0.05,
+  varfunc = NULL)
+{
+  if (length(object$coef) > 2)
+    stop("More than one independent variable in your model - not implemented")
+
+  if (alpha <= 0 | alpha >= 1)
+    stop("Alpha should be between 0 and 1 (exclusive)")
+
+  m <- object
+  level <- 1 - alpha
+  y <- m$model[[1]]
+  x <- m$model[[2]]
+  if (xlim[1] == "auto") xlim[1] <- 0
+  if (xlim[2] == "auto") xlim[2] <- max(x)
+  xlim <- as.numeric(xlim)
+  newdata <- list(
+    x = seq(from = xlim[[1]], to = xlim[[2]], length=250))
+  names(newdata) <- names(m$model)[[2]]
+  if (is.null(varfunc)) {
+    varfunc <- if (length(m$weights)) {
+        function(variable) mean(m$weights)
+      } else function(variable) rep(1,250)
+  }
+  pred.lim <- predict(m, newdata, interval = "prediction",
+    level=level, weights.newdata = varfunc(m))
+  conf.lim <- predict(m, newdata, interval = "confidence",
+    level=level)
+  yrange.auto <- range(c(0,pred.lim))
+  if (ylim[1] == "auto") ylim[1] <- yrange.auto[1]
+  if (ylim[2] == "auto") ylim[2] <- yrange.auto[2]
+  plot(1,
+    type = "n", 
+    xlab = xlab,
+    ylab = ylab,
+    xlim = as.numeric(xlim),
+    ylim = as.numeric(ylim)
+  )
+  points(x,y, pch = 21, bg = "yellow")
+  matlines(newdata[[1]], pred.lim, lty = c(1, 4, 4), 
+    col = c("black", "red", "red"))
+  if (length(object$weights) > 0) {
+    legend(min(x), 
+      max(pred.lim, na.rm = TRUE), 
+      legend = c("Fitted Line", "Confidence Bands"),
+      lty = c(1, 3), 
+      lwd = 2, 
+      col = c("black", "green4"), 
+      horiz = FALSE, cex = 0.9, bg = "gray95")
+  } else {
+  matlines(newdata[[1]], conf.lim, lty = c(1, 3, 3), 
+    col = c("black", "green4", "green4"))
+  legend(min(x), 
+    max(pred.lim, na.rm = TRUE), 
+    legend = c("Fitted Line", "Confidence Bands", 
+        "Prediction Bands"), 
+    lty = c(1, 3, 4), 
+    lwd = 2, 
+    col = c("black", "green4", "red"), 
+    horiz = FALSE, cex = 0.9, bg = "gray95")
+  }
+}