From 513dfbdcdda94a901b5901b486ff5500c7d158b1 Mon Sep 17 00:00:00 2001
From: ranke <ranke@5fad18fb-23f0-0310-ab10-e59a3bee62b4>
Date: Wed, 10 May 2006 15:44:14 +0000
Subject: The inverse prediction works in a variety of cases and is tested with
 Examples 7 and 8 from Massart!

I need to compare with the DIN and draper examples, and finish
the package vignette.



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/chemCal@6 5fad18fb-23f0-0310-ab10-e59a3bee62b4
---
 R/calplot.R            | 52 +++++++++++++++++++++++++++
 R/chemCal.R            | 95 --------------------------------------------------
 R/inverse.predict.lm.R | 95 ++++++++++++++++++++++++++++++++++++++------------
 3 files changed, 124 insertions(+), 118 deletions(-)
 create mode 100644 R/calplot.R
 delete mode 100644 R/chemCal.R

(limited to 'R')

diff --git a/R/calplot.R b/R/calplot.R
new file mode 100644
index 0000000..cea1149
--- /dev/null
+++ b/R/calplot.R
@@ -0,0 +1,52 @@
+calplot <- function(object, xlim = "auto", ylim = "auto", 
+  xlab = "Concentration", ylab = "Response", alpha=0.05)
+{
+  UseMethod("calplot")
+}
+
+calplot.default <- function(object, xlim = "auto", ylim = "auto", 
+  xlab = "Concentration", ylab = "Response", alpha=0.05)
+{
+  stop("Calibration plots only implemented for univariate lm objects.")
+}
+
+calplot.lm <- function(object, xlim = "auto", ylim = "auto", 
+  xlab = "Concentration", ylab = "Response", alpha=0.05)
+{
+  if (length(object$coef) > 2)
+    stop("More than one independent variable in your model - not implemented")
+
+  if (alpha <= 0 | alpha >= 1)
+    stop("Alpha should be between 0 and 1 (exclusive)")
+
+  m <- object
+  level <- 1 - alpha
+  x <- m$model$x
+  y <- m$model$y
+  newdata <- data.frame(x = seq(0,max(x),length=250))
+  pred.lim <- predict(m, newdata, interval = "prediction",level=level)
+  conf.lim <- predict(m, newdata, interval = "confidence",level=level)
+  if (xlim == "auto") xlim = c(0,max(x))
+  if (ylim == "auto") ylim = range(c(pred.lim,y))
+  plot(1,
+    type = "n", 
+    xlab = xlab,
+    ylab = ylab,
+    xlim = xlim,
+    ylim = ylim
+  )
+  points(x,y, pch = 21, bg = "yellow")
+  matlines(newdata$x, pred.lim, lty = c(1, 4, 4), 
+    col = c("black", "red", "red"))
+  matlines(newdata$x, conf.lim, lty = c(1, 3, 3), 
+    col = c("black", "green4", "green4"))
+
+  legend(min(x), 
+    max(pred.lim, na.rm = TRUE), 
+    legend = c("Fitted Line", "Confidence Bands", 
+        "Prediction Bands"), 
+    lty = c(1, 3, 4), 
+    lwd = 2, 
+    col = c("black", "green4", "red"), 
+    horiz = FALSE, cex = 0.9, bg = "gray95")
+}
diff --git a/R/chemCal.R b/R/chemCal.R
deleted file mode 100644
index fab7db4..0000000
--- a/R/chemCal.R
+++ /dev/null
@@ -1,95 +0,0 @@
-calm <- function(data)
-{
-    y <- data[[2]]
-    x <- data[[1]]
-    m <- lm(y ~ x)
-    s <- summary(m)
-    if (s$coefficients[1,4] > 0.05) 
-    {
-        m <- lm(y ~ x - 1)
-        s <- summary(m)
-        m$intercept <- FALSE
-    } else {
-        m$intercept <- TRUE
-    }
-    class(m) <- "calm"
-    m$yname <- names(data)[[1]]
-    m$xname <- names(data)[[2]]
-    return(m)    
-}
-predict.calm <- predict.lm
-print.calm <- print.lm
-summary.calm <- summary.lm
-plot.calm <- function(x,...,
-    xunit="",yunit="",measurand="",
-    level=0.95)
-{
-    m <- x
-    x <- m$model$x
-    y <- m$model$y
-    newdata <- data.frame(x = seq(0,max(x),length=250))
-    pred.lim <- predict(m, newdata, interval = "prediction",level=level)
-    conf.lim <- predict(m, newdata, interval = "confidence",level=level)
-    if (xunit!="") {
-        xlab <- paste("Concentration in ",xunit)
-    } else xlab <- m$xname
-    if (yunit=="") yunit <- m$yname
-    if (measurand!="") {
-        main <- paste("Calibration for",measurand)
-    } else main <- "Calibration"
-    plot(1,
-        xlab = xlab,
-        ylab = yunit,
-        type = "n", 
-        main = main,
-        xlim = c(0,max(x)), 
-        ylim = range(pred.lim)
-    )
-    points(x,y, pch = 21, bg = "yellow")
-    matlines(newdata$x, pred.lim, lty = c(1, 4, 4), 
-        col = c("black", "red", "red"))
-    matlines(newdata$x, 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")
-}
-predictx <- function(m,yobs,level=0.95)
-{
-    s <- summary(m)    
-    xi <- m$model$x
-    yi <- m$model$y
-    n <- length(yi)
-    p <- length(yobs)
-    if (p > 1) {
-        varyobs <- var(yobs)
-    } else {
-        varyobs <- 0
-    }
-    if (!m$intercept) {
-        b1 <- summary(m)$coef["x","Estimate"]
-        varb1 <- summary(m)$coef["x","Std. Error"]^2
-        xpred <- mean(yobs)/b1
-        varxpred <- (varyobs + xpred^2 * varb1) / b1^2
-        sdxpred <- sqrt(varxpred) 
-    } else 
-    {
-        b0 <- summary(m)$coef["(Intercept)","Estimate"]
-        b1 <- summary(m)$coef["x","Estimate"]
-        S <- summary(m)$sigma
-        xpred <- (mean(yobs) - b0)/b1
-        sumxxbar <- sum((xi - mean(xi))^2) 
-        yybar <- (mean(yobs) - mean(yi))^2
-        sdxpred <- (S/b1) * (1/p + 1/n + yybar/(b1^2 * sumxxbar))^0.5
-    }
-    t <- qt((1 + level)/2,n - 2)
-    confxpred <- t * sdxpred
-
-    result <- c(estimate=xpred,sdxpred=sdxpred,confxpred=confxpred)
-}
diff --git a/R/inverse.predict.lm.R b/R/inverse.predict.lm.R
index f438d99..f1921e4 100644
--- a/R/inverse.predict.lm.R
+++ b/R/inverse.predict.lm.R
@@ -1,40 +1,89 @@
 # This is an implementation of Equation (8.28) in the Handbook of Chemometrics
-# and Qualimetrics, Part A, Massart et al, page 200, validated with Example 8
-# on the same page
+# and Qualimetrics, Part A, Massart et al (1997), page 200, validated with
+# Example 8 on the same page
 
-inverse.predict <- function(object, newdata, alpha=0.05)
+inverse.predict <- function(object, newdata, 
+  ws = ifelse(length(object$weights) > 0, mean(object$weights), 1),
+  alpha=0.05, ss = "auto")
 {
   UseMethod("inverse.predict")
 }
 
-inverse.predict.default <- function(object, newdata, alpha=0.05)
+inverse.predict.default <- function(object, newdata, 
+  ws = ifelse(length(object$weights) > 0, mean(object$weights), 1),
+  alpha=0.05, ss = "auto")
 {
   stop("Inverse prediction only implemented for univariate lm objects.")
 }
 
-inverse.predict.lm <- function(object, newdata, alpha=0.05)
+inverse.predict.lm <- function(object, newdata, 
+  ws = ifelse(length(object$weights) > 0, mean(object$weights), 1),
+  alpha=0.05, ss = "auto")
 {
-  if (is.list(newdata)) {
-    if (!is.null(newdata$y))
-      newdata <- newdata$y
-    else
-      stop("Newdata list should contain element newdata$y")
-  }
+  if (length(object$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)")
+
+  ybars <- mean(newdata)
+  m <- length(newdata)
 
-  if (is.matrix(newdata)) {
-    Y <- newdata
-    Ybar <- apply(Y,1,mean)
-    nrepl <- ncol(Y)
+  yx <- split(object$model$y,object$model$x)
+  n <- length(yx)
+  x <- as.numeric(names(yx))
+  ybar <- sapply(yx,mean)
+  if (length(object$weights) > 0) {
+    wx <- split(object$weights,object$model$x)
+    w <- sapply(wx,mean)
+  } else {
+    w <- rep(1,n)
   }
-  else {
-    Y <- as.vector(newdata)
-    Ybar <- Y
-    nrepl <- 1 
+  yhatx <- split(object$fitted.values,object$model$x)
+  yhat <- sapply(yhatx,mean)
+  se <- sqrt(sum(w*(ybar - yhat)^2)/(n-2))
+  if (ss == "auto") {
+    ss <- se
+  } else {
+    ss <- ss
   }
 
-  if (length(object$coef) > 2)
-    stop("Inverse prediction not yet implemented for more than one independent variable")
+  b1 <- object$coef[["x"]]
 
-  if (alpha <= 0 | alpha >= 1)
-    stop("Alpha should be between 0 and 1 (exclusive)")
+  ybarw <- sum(w * ybar)/sum(w)
+
+# The commented out code for sxhats is equation 8.28 without changes.  It has
+# been replaced by the code below, in order to be able to take into account a
+# precision in the sample measurements that differs from the precision in the
+# calibration samples.
+
+#  sxhats <- se/b1 * sqrt(
+#    1/(ws * m) + 
+#    1/sum(w) + 
+#    (ybars - ybarw)^2 * sum(w) /
+#      (b1^2 * (sum(w) * sum(w * x^2) - sum(w * x)^2))
+#  )
+
+# This is equation 8.28, but with the possibility to take into account a 
+# different precision measurement of the sample and standard solutions
+# in analogy to equation 8.26
+  sxhats <- 1/b1 * sqrt(
+    ss^2/(ws * m) + 
+    se^2 * (1/sum(w) + 
+      (ybars - ybarw)^2 * sum(w) /
+        (b1^2 * (sum(w) * sum(w * x^2) - sum(w * x)^2)))
+  )
+
+  if (names(object$coef)[1] == "(Intercept)") {
+    b0 <- object$coef[["(Intercept)"]]
+  } else {
+    b0 <- 0
+  }
+
+  xs <- (ybars - b0) / b1
+  t <- qt(1-0.5*alpha, n - 2)
+  conf <- t * sxhats
+  result <- list("Prediction"=xs,"Standard Error"=sxhats,
+    "Confidence"=conf, "Confidence Limits"=c(xs - conf, xs + conf))
+  return(result)
 }
-- 
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