- Added the tolerance argument and the fix to the call to optimize() also in

  loq()
- Version 0.1-33 just submitted to CRAN




git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/chemCal@33 5fad18fb-23f0-0310-ab10-e59a3bee62b4

7 files changed, 29 insertions, 23 deletions

diff --git a/branches/0.1/chemCal/ChangeLog b/branches/0.1/chemCal/ChangeLog
index 852b753..c258c26 100644
--- a/branches/0.1/chemCal/ChangeLog
+++ b/branches/0.1/chemCal/ChangeLog
@@ -1,11 +1,11 @@
-2014-04-24  Johannes Ranke <jranke@uni-bremen.de> for chemCal (0.1-32)

+2014-04-24  Johannes Ranke <jranke@uni-bremen.de> for chemCal (0.1-33)

 

-	* Bugfix in lod(): In the case of small absolute x values (e.g. on the order

-	of 1e-4 and smaller), the lod calculated using the default method could

-	produce inaccurate results as the default tolerance that was used in the

-	internal call to optimize is inappropriate in such cases. Now a reasonable

-	default is used which can be overriden by the user. Thanks to Jérôme

-	Ambroise for reporting the bug.

+	* Bugfix in lod() and loq(): In the case of small absolute x values (e.g. on

+	the order of 1e-4 and smaller), the lod or loq calculated using the default

+	method could produce inaccurate results as the default tolerance that was

+	used in the internal call to optimize is inappropriate in such cases. Now a

+	reasonable default is used which can be overriden by the user. Thanks to

+	Jérôme Ambroise for reporting the bug.

 

 Changes performed in earlier versions are documented in the subversion log

 files found at http://kriemhild.uft.uni-bremen.de/viewcvs/?root=chemCal

diff --git a/branches/0.1/chemCal/DESCRIPTION b/branches/0.1/chemCal/DESCRIPTION
index 900c92a..13d5bc6 100644
--- a/branches/0.1/chemCal/DESCRIPTION
+++ b/branches/0.1/chemCal/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: chemCal
-Version: 0.1-32
+Version: 0.1-33
 Date: 2014-04-24
 Title: Calibration functions for analytical chemistry
 Author: Johannes Ranke <jranke@uni-bremen.de>
diff --git a/branches/0.1/chemCal/R/loq.R b/branches/0.1/chemCal/R/loq.R
index 5776096..f832265 100644
--- a/branches/0.1/chemCal/R/loq.R
+++ b/branches/0.1/chemCal/R/loq.R
@@ -1,17 +1,17 @@
 loq <- function(object, ..., alpha = 0.05, k = 3, n = 1, w.loq = "auto", 
-  var.loq = "auto")
+  var.loq = "auto", tol = "default")
 {
   UseMethod("loq")
 }
 
 loq.default <- function(object, ..., alpha = 0.05, k = 3, n = 1, w.loq = "auto",
-  var.loq = "auto")
+  var.loq = "auto", tol = "default")
 {
   stop("loq is only implemented for univariate lm objects.")
 }
 
 loq.lm <- function(object, ..., alpha = 0.05, k = 3, n = 1, w.loq = "auto",
-  var.loq = "auto")
+  var.loq = "auto", tol = "default")
 {
   if (length(object$weights) > 0 && var.loq == "auto" && w.loq == "auto") {
     stop(paste("If you are using a model from weighted regression,",
@@ -20,6 +20,7 @@ loq.lm <- function(object, ..., alpha = 0.05, k = 3, n = 1, w.loq = "auto",
       "limit of quantification"))
   }
   xname <- names(object$model)[[2]]
+  xvalues <- object$model[[2]]
   yname <- names(object$model)[[1]]
   f <- function(x) {
     newdata <- data.frame(x = x)
@@ -29,8 +30,8 @@ loq.lm <- function(object, ..., alpha = 0.05, k = 3, n = 1, w.loq = "auto",
         var.s = var.loq, alpha = alpha)
     (p[["Prediction"]] - k * p[["Confidence"]])^2
   }
-  tmp <- optimize(f,interval=c(0,max(object$model[[2]])))
-  loq.x <- tmp$minimum
+  if (tol == "default") tol = min(xvalues[xvalues !=0]) / 1000
+  loq.x <- optimize(f, interval = c(0, max(xvalues) * 10), tol = tol)$minimum
   newdata <- data.frame(x = loq.x)
   names(newdata) <- xname
   loq.y <- predict(object, newdata)
diff --git a/branches/0.1/chemCal/man/lod.Rd b/branches/0.1/chemCal/man/lod.Rd
index 918e820..04aac1f 100644
--- a/branches/0.1/chemCal/man/lod.Rd
+++ b/branches/0.1/chemCal/man/lod.Rd
@@ -33,8 +33,8 @@
   }
   \item{tol}{
     When the \dQuote{default} method is used, the default tolerance
-    for the lod on the x scale is the value of the smallest non-zero standard
-    divided by 1000.
+    for the LOD on the x scale is the value of the smallest non-zero standard
+    divided by 1000. Can be set to a numeric value to override this.
   }
 }
 \value{
diff --git a/branches/0.1/chemCal/man/loq.Rd b/branches/0.1/chemCal/man/loq.Rd
index 7541e77..082cf34 100644
--- a/branches/0.1/chemCal/man/loq.Rd
+++ b/branches/0.1/chemCal/man/loq.Rd
@@ -6,7 +6,7 @@
 \title{Estimate a limit of quantification (LOQ)}
 \usage{
   loq(object, \dots, alpha = 0.05, k = 3, n = 1, w.loq = "auto",
-    var.loq = "auto")
+    var.loq = "auto", tol = "default")
 }
 \arguments{
   \item{object}{
@@ -43,6 +43,11 @@
     The approximate variance at the LOQ. The default value is 
     calculated from the model.
   }
+  \item{tol}{
+    The default tolerance for the LOQ on the x scale is the value of the
+    smallest non-zero standard divided by 1000. Can be set to a 
+    numeric value to override this.
+  }
 }
 \value{
   The estimated limit of quantification for a model used for calibration.
diff --git a/branches/0.1/chemCal/tests/din32645.Rout.save b/branches/0.1/chemCal/tests/din32645.Rout.save
index d7c6102..7c9e55d 100644
--- a/branches/0.1/chemCal/tests/din32645.Rout.save
+++ b/branches/0.1/chemCal/tests/din32645.Rout.save
@@ -45,4 +45,4 @@ $y
 > 
 > proc.time()
    user  system elapsed 
-  0.454   0.286   0.341 
+  0.472   0.302   0.354 
diff --git a/branches/0.1/chemCal/tests/massart97.Rout.save b/branches/0.1/chemCal/tests/massart97.Rout.save
index f00ae97..ce99c30 100644
--- a/branches/0.1/chemCal/tests/massart97.Rout.save
+++ b/branches/0.1/chemCal/tests/massart97.Rout.save
@@ -108,21 +108,21 @@ $y
 > 
 > loq(m0)
 $x
-[1] 13.97767
+[1] 13.97764
 
 $y
-       1 
-30.62355 
+      1 
+30.6235 
 
 > loq(m, w.loq = 1.67)
 $x
-[1] 7.346231
+[1] 7.346195
 
 $y
        1 
-17.90784 
+17.90777 
 
 > 
 > proc.time()
    user  system elapsed 
-  0.516   0.344   0.412 
+  0.529   0.327   0.443