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| -rw-r--r-- | branches/0.1/chemCal/ChangeLog | 11 | ||||
| -rw-r--r-- | branches/0.1/chemCal/DESCRIPTION | 4 | ||||
| -rw-r--r-- | branches/0.1/chemCal/INDEX | 9 | ||||
| -rw-r--r-- | branches/0.1/chemCal/NAMESPACE | 6 | ||||
| -rw-r--r-- | branches/0.1/chemCal/R/lod.R | 10 | ||||
| -rw-r--r-- | branches/0.1/chemCal/man/lod.Rd | 9 | ||||
| -rw-r--r-- | branches/0.1/chemCal/tests/din32645.Rout.save | 12 | ||||
| -rw-r--r-- | branches/0.1/chemCal/tests/massart97.Rout.save | 12 | ||||
| -rw-r--r-- | branches/0.1/chemCal/vignettes/Rplots.ps | 1970 | ||||
| -rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal-001.eps | 1762 | ||||
| -rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal-002.eps | 288 | ||||
| -rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal.aux | 18 | ||||
| -rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal.bbl | 0 | ||||
| -rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal.blg | 46 | ||||
| -rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal.log | 399 | ||||
| -rw-r--r-- | branches/0.1/chemCal/vignettes/chemCal.out | 0 |
16 files changed, 46 insertions, 4510 deletions
diff --git a/branches/0.1/chemCal/ChangeLog b/branches/0.1/chemCal/ChangeLog new file mode 100644 index 0000000..852b753 --- /dev/null +++ b/branches/0.1/chemCal/ChangeLog @@ -0,0 +1,11 @@ +2014-04-24 Johannes Ranke <jranke@uni-bremen.de> for chemCal (0.1-32)
+
+ * 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.
+
+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 4eb98c2..900c92a 100644 --- a/branches/0.1/chemCal/DESCRIPTION +++ b/branches/0.1/chemCal/DESCRIPTION @@ -1,6 +1,6 @@ Package: chemCal -Version: 0.1-29 -Date: 2013-05-31 +Version: 0.1-32 +Date: 2014-04-24 Title: Calibration functions for analytical chemistry Author: Johannes Ranke <jranke@uni-bremen.de> Maintainer: Johannes Ranke <jranke@uni-bremen.de> diff --git a/branches/0.1/chemCal/INDEX b/branches/0.1/chemCal/INDEX deleted file mode 100644 index f880eb6..0000000 --- a/branches/0.1/chemCal/INDEX +++ /dev/null @@ -1,9 +0,0 @@ -calplot Plot calibration graphs from univariate linear - models -chemCal-package Calibration functions for analytical chemistry -din32645 Calibration data from DIN 32645 -inverse.predict Predict x from y for a linear calibration -lod Estimate a limit of detection (LOD) -loq Estimate a limit of quantification (LOQ) -massart97ex3 Calibration data from Massart et al. (1997), - example 3 diff --git a/branches/0.1/chemCal/NAMESPACE b/branches/0.1/chemCal/NAMESPACE new file mode 100644 index 0000000..6314e29 --- /dev/null +++ b/branches/0.1/chemCal/NAMESPACE @@ -0,0 +1,6 @@ +# Export all names +exportPattern(".") +S3method(lod, lm) +S3method(loq, lm) +S3method(inverse.predict, lm) +S3method(inverse.predict, rlm) diff --git a/branches/0.1/chemCal/R/lod.R b/branches/0.1/chemCal/R/lod.R index f5bbb7d..5b74418 100644 --- a/branches/0.1/chemCal/R/lod.R +++ b/branches/0.1/chemCal/R/lod.R @@ -1,14 +1,14 @@ -lod <- function(object, ..., alpha = 0.05, beta = 0.05, method = "default") +lod <- function(object, ..., alpha = 0.05, beta = 0.05, method = "default", tol = "default") { UseMethod("lod") } -lod.default <- function(object, ..., alpha = 0.05, beta = 0.05, method = "default") +lod.default <- function(object, ..., alpha = 0.05, beta = 0.05, method = "default", tol = "default") { stop("lod is only implemented for univariate lm objects.") } -lod.lm <- function(object, ..., alpha = 0.05, beta = 0.05, method = "default") +lod.lm <- function(object, ..., alpha = 0.05, beta = 0.05, method = "default", tol = "default") { if (length(object$weights) > 0) { stop(paste( @@ -21,6 +21,7 @@ lod.lm <- function(object, ..., alpha = 0.05, beta = 0.05, method = "default") )) } xname <- names(object$model)[[2]] + xvalues <- object$model[[2]] yname <- names(object$model)[[1]] newdata <- data.frame(0) names(newdata) <- xname @@ -42,7 +43,8 @@ lod.lm <- function(object, ..., alpha = 0.05, beta = 0.05, method = "default") yd <- pi.y[[1,"lwr"]] (yd - yc)^2 } - lod.x <- optimize(f,interval=c(0,max(object$model[[xname]])))$minimum + if (tol == "default") tol = min(xvalues[xvalues !=0]) / 1000 + lod.x <- optimize(f, interval = c(0, max(xvalues) * 10), tol = tol)$minimum newdata <- data.frame(x = lod.x) names(newdata) <- xname lod.y <- predict(object, newdata) diff --git a/branches/0.1/chemCal/man/lod.Rd b/branches/0.1/chemCal/man/lod.Rd index e468e1d..918e820 100644 --- a/branches/0.1/chemCal/man/lod.Rd +++ b/branches/0.1/chemCal/man/lod.Rd @@ -5,7 +5,7 @@ \alias{lod.default} \title{Estimate a limit of detection (LOD)} \usage{ - lod(object, \dots, alpha = 0.05, beta = 0.05, method = "default") + lod(object, \dots, alpha = 0.05, beta = 0.05, method = "default", tol = "default") } \arguments{ \item{object}{ @@ -25,12 +25,17 @@ The error tolerance beta for the detection limit. } \item{method}{ - The default method uses a prediction interval at the LOD + The \dQuote{default} method uses a prediction interval at the LOD for the estimation of the LOD, which obviously requires iteration. This is described for example in Massart, p. 432 ff. The \dQuote{din} method uses the prediction interval at x = 0 as an approximation. } + \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. + } } \value{ A list containig the corresponding x and y values of the estimated limit of diff --git a/branches/0.1/chemCal/tests/din32645.Rout.save b/branches/0.1/chemCal/tests/din32645.Rout.save index 00ae02e..d7c6102 100644 --- a/branches/0.1/chemCal/tests/din32645.Rout.save +++ b/branches/0.1/chemCal/tests/din32645.Rout.save @@ -1,7 +1,6 @@ -R version 2.13.1 (2011-07-08) -Copyright (C) 2011 The R Foundation for Statistical Computing -ISBN 3-900051-07-0 +R version 3.1.0 (2014-04-10) -- "Spring Dance" +Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. @@ -36,11 +35,14 @@ $`Confidence Limits` > lod <- lod(m, alpha = 0.01, beta = 0.5) > lod(m, alpha = 0.01, beta = 0.01) $x -[1] 0.132904 +[1] 0.132909 $y 1 -3764.977 +3765.025 > loq <- loq(m, alpha = 0.01) > +> proc.time() + user system elapsed + 0.454 0.286 0.341 diff --git a/branches/0.1/chemCal/tests/massart97.Rout.save b/branches/0.1/chemCal/tests/massart97.Rout.save index 740dd18..f00ae97 100644 --- a/branches/0.1/chemCal/tests/massart97.Rout.save +++ b/branches/0.1/chemCal/tests/massart97.Rout.save @@ -1,7 +1,6 @@ -R version 2.13.1 (2011-07-08) -Copyright (C) 2011 The R Foundation for Statistical Computing -ISBN 3-900051-07-0 +R version 3.1.0 (2014-04-10) -- "Spring Dance" +Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. @@ -100,11 +99,11 @@ $`Confidence Limits` > m0 <- lm(y ~ x) > lod(m0) $x -[1] 5.406637 +[1] 5.407085 $y 1 -13.63822 +13.63911 > > loq(m0) @@ -124,3 +123,6 @@ $y 17.90784 > +> proc.time() + user system elapsed + 0.516 0.344 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