From cf329866248fab96ea60d1d7ee20562a3da2eb54 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 4 Oct 2016 08:46:58 +0200 Subject: Remove old version of static documentation --- inst/web/calplot.lm-2.png | Bin 21704 -> 0 bytes inst/web/calplot.lm.html | 166 - inst/web/chemCal-package.html | 96 - inst/web/css/bootstrap-responsive.css | 815 ----- inst/web/css/bootstrap-responsive.min.css | 9 - inst/web/css/bootstrap.css | 4983 --------------------------- inst/web/css/bootstrap.min.css | 9 - inst/web/css/highlight.css | 28 - inst/web/css/staticdocs.css | 18 - inst/web/din32645-2.png | Bin 19881 -> 0 bytes inst/web/din32645.html | 194 -- inst/web/img/glyphicons-halflings-white.png | Bin 8777 -> 0 bytes inst/web/img/glyphicons-halflings.png | Bin 13826 -> 0 bytes inst/web/index.html | 143 - inst/web/inverse.predict.html | 202 -- inst/web/js/bootstrap.js | 1825 ---------- inst/web/js/bootstrap.min.js | 6 - inst/web/lod.html | 198 -- inst/web/loq.html | 189 - inst/web/massart97ex1.html | 98 - inst/web/massart97ex3-5.png | Bin 16476 -> 0 bytes inst/web/massart97ex3.html | 198 -- inst/web/vignettes/chemCal.pdf | Bin 165905 -> 0 bytes 23 files changed, 9177 deletions(-) delete mode 100644 inst/web/calplot.lm-2.png delete mode 100644 inst/web/calplot.lm.html delete mode 100644 inst/web/chemCal-package.html delete mode 100644 inst/web/css/bootstrap-responsive.css delete mode 100644 inst/web/css/bootstrap-responsive.min.css delete mode 100644 inst/web/css/bootstrap.css delete mode 100644 inst/web/css/bootstrap.min.css delete mode 100644 inst/web/css/highlight.css delete mode 100644 inst/web/css/staticdocs.css delete mode 100644 inst/web/din32645-2.png delete mode 100644 inst/web/din32645.html delete mode 100644 inst/web/img/glyphicons-halflings-white.png delete mode 100644 inst/web/img/glyphicons-halflings.png delete mode 100644 inst/web/index.html delete mode 100644 inst/web/inverse.predict.html delete mode 100644 inst/web/js/bootstrap.js delete mode 100644 inst/web/js/bootstrap.min.js delete mode 100644 inst/web/lod.html delete mode 100644 inst/web/loq.html delete mode 100644 inst/web/massart97ex1.html delete mode 100644 inst/web/massart97ex3-5.png delete mode 100644 inst/web/massart97ex3.html delete mode 100644 inst/web/vignettes/chemCal.pdf (limited to 'inst') diff --git a/inst/web/calplot.lm-2.png b/inst/web/calplot.lm-2.png deleted file mode 100644 index db7fe6e..0000000 Binary files a/inst/web/calplot.lm-2.png and /dev/null differ diff --git a/inst/web/calplot.lm.html b/inst/web/calplot.lm.html deleted file mode 100644 index a8d3f4b..0000000 --- a/inst/web/calplot.lm.html +++ /dev/null @@ -1,166 +0,0 @@ - - - - -calplot. chemCal 0.1-37 - - - - - - - - - - - - - - - - - -
-
- -
- -

Plot calibration graphs from univariate linear models

- -
-
-

Usage

-
calplot(object, xlim = c("auto", "auto"), ylim = c("auto", "auto"), xlab = "Concentration", ylab = "Response", alpha=0.05, varfunc = NULL)
- -

Arguments

-
-
object
-
- A univariate model object of class lm or - rlm - with model formula y ~ x or y ~ x - 1. -
-
xlim
-
- The limits of the plot on the x axis. -
-
ylim
-
- The limits of the plot on the y axis. -
-
xlab
-
- The label of the x axis. -
-
ylab
-
- The label of the y axis. -
-
alpha
-
- The error tolerance level for the confidence and prediction bands. Note that this - includes both tails of the Gaussian distribution, unlike the alpha and beta parameters - used in lod (see note below). -
-
varfunc
-
- The variance function for generating the weights in the model. - Currently, this argument is ignored (see note below). -
-
- -
-

Description

- -

Produce graphics of calibration data, the fitted model as well - as confidence, and, for unweighted regression, prediction bands.

- -
- -
-

Value

- -

- A plot of the calibration data, of your fitted model as well as lines showing - the confidence limits. Prediction limits are only shown for models from - unweighted regression. -

- -
- -
-

Note

- -

Prediction bands for models from weighted linear regression require weights - for the data, for which responses should be predicted. Prediction intervals - using weights e.g. from a variance function are currently not supported by - the internally used function predict.lm, therefore, - calplot does not draw prediction bands for such models.

- -

It is possible to compare the calplot prediction bands with the - lod values if the lod() alpha and beta parameters are - half the value of the calplot() alpha parameter.

- -

- -
- -

Examples

-
data(massart97ex3) -m <- lm(y ~ x, data = massart97ex3) -calplot(m) -
-

-
-
- - - -

Author

- - Johannes Ranke - jranke@uni-bremen.de - http://www.uft.uni-bremen.de/chemie/ranke - - -
-
- - -
- - \ No newline at end of file diff --git a/inst/web/chemCal-package.html b/inst/web/chemCal-package.html deleted file mode 100644 index def6014..0000000 --- a/inst/web/chemCal-package.html +++ /dev/null @@ -1,96 +0,0 @@ - - - - -chemCal-package. chemCal 0.1-37 - - - - - - - - - - - - - - - - - -
-
- -
- -

- Calibration functions for analytical chemistry -

- -
-
- -
-

Description

- -

See ../DESCRIPTION

- -
- -
-

Details

- -

There is a package vignette located in ../doc/chemCal.pdf.

- -
-
-
- - - -

Author

- - Author and Maintainer: Johannes Ranke - - -
-
- - -
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{margin-bottom: 0.5em; clear: both;} - -footer { - margin-top: 45px; - padding: 35px 0 36px; - border-top: 1px solid #e5e5e5; -} -footer p { - margin-bottom: 0; - color: #555; -} diff --git a/inst/web/din32645-2.png b/inst/web/din32645-2.png deleted file mode 100644 index 306c8cf..0000000 Binary files a/inst/web/din32645-2.png and /dev/null differ diff --git a/inst/web/din32645.html b/inst/web/din32645.html deleted file mode 100644 index 7d42e8f..0000000 --- a/inst/web/din32645.html +++ /dev/null @@ -1,194 +0,0 @@ - - - - -din32645. chemCal 0.1-37 - - - - - - - - - - - - - - - - - -
-
- -
- -

Calibration data from DIN 32645

- -
-
-

Usage

-
data(din32645)
- -
-

Description

- -

Sample dataset to test the package.

- -
- -
-

Format

- -

A dataframe containing 10 rows of x and y values.

- -
- -
-

References

- -

DIN 32645 (equivalent to ISO 11843), Beuth Verlag, Berlin, 1994

- -

Dintest. Plugin for MS Excel for evaluations of calibration data. Written - by Georg Schmitt, University of Heidelberg. Formerly available from - the Website of the University of Heidelberg.

- -

Currie, L. A. (1997) Nomenclature in evaluation of analytical methods including - detection and quantification capabilities (IUPAC Recommendations 1995). - Analytica Chimica Acta 391, 105 - 126.

- -
- -

Examples

-
data(din32645) -m <- lm(y ~ x, data = din32645) -calplot(m) -
-

-
-## Prediction of x with confidence interval -(prediction <- inverse.predict(m, 3500, alpha = 0.01)) -
-
$Prediction -[1] 0.1054792 - -$`Standard Error` -[1] 0.02215619 - -$Confidence -[1] 0.07434261 - -$`Confidence Limits` -[1] 0.03113656 0.17982178 - -
-
-# This should give 0.07434 according to test data from Dintest, which -# was collected from Procontrol 3.1 (isomehr GmbH) in this case -round(prediction$Confidence,5) -
-
[1] 0.07434 -
-
-## Critical value: -(crit <- lod(m, alpha = 0.01, beta = 0.5)) -
-
$x -[1] 0.0698127 - -$y - 1 -3155.393 - -
-
-# According to DIN 32645, we should get 0.07 for the critical value -# (decision limit, "Nachweisgrenze") -round(crit$x, 2) -
-
[1] 0.07 -
-
# and according to Dintest test data, we should get 0.0698 from -round(crit$x, 4) -
-
[1] 0.0698 -
-
-## Limit of detection (smallest detectable value given alpha and beta) -# In German, the smallest detectable value is the "Erfassungsgrenze", and we -# should get 0.14 according to DIN, which we achieve by using the method -# described in it: -lod.din <- lod(m, alpha = 0.01, beta = 0.01, method = "din") -round(lod.din$x, 2) -
-
[1] 0.14 -
-
-## Limit of quantification -# This accords to the test data coming with the test data from Dintest again, -# except for the last digits of the value cited for Procontrol 3.1 (0.2121) -(loq <- loq(m, alpha = 0.01)) -
-
$x -[1] 0.2119575 - -$y - 1 -4528.787 - -
-
round(loq$x,4) -
-
[1] 0.212 -
-
-# A similar value is obtained using the approximation -# LQ = 3.04 * LC (Currie 1999, p. 120) -3.04 * lod(m,alpha = 0.01, beta = 0.5)$x -
-
[1] 0.2122306 -
-
-
- - - -
-
- - -
- - \ No newline at end of file diff --git a/inst/web/img/glyphicons-halflings-white.png b/inst/web/img/glyphicons-halflings-white.png deleted file mode 100644 index 3bf6484..0000000 Binary files a/inst/web/img/glyphicons-halflings-white.png and /dev/null differ diff --git a/inst/web/img/glyphicons-halflings.png b/inst/web/img/glyphicons-halflings.png deleted file mode 100644 index 79bc568..0000000 Binary files a/inst/web/img/glyphicons-halflings.png and /dev/null differ diff --git a/inst/web/index.html b/inst/web/index.html deleted file mode 100644 index 501c0d4..0000000 --- a/inst/web/index.html +++ /dev/null @@ -1,143 +0,0 @@ - - - - -Index. chemCal 0.1-37 - - - - - - - - - - - - - - - - - -
-
- -
- -
-
- Simple functions for plotting linear -calibration functions and estimating standard errors for measurements -according to the Handbook of Chemometrics and Qualimetrics: Part A -by Massart et al. There are also functions estimating the limit -of detection (LOD) and limit of quantification (LOQ). -The functions work on model objects from - optionally weighted - linear -regression (lm) or robust linear regression ('rlm' from the 'MASS' package). - -

Help topics

- -

Main functions

-

Essential functionality

- - -
    - -
  • - inverse.predict(inverse.predict.lm, inverse.predict.rlm, inverse.predict.default)
    Predict x from y for a linear calibration
  • - -
  • - calplot(calplot.default, calplot.lm)
    Plot calibration graphs from univariate linear models
  • - -
-

LOD and LOQ

-

Limit of detection and limit of quantification

- - -
    - -
  • - lod(lod.lm, lod.rlm, lod.default)
    Estimate a limit of detection (LOD)
  • - -
  • - loq(loq.lm, loq.rlm, loq.default)
    Estimate a limit of quantification (LOQ)
  • - -
-

Datasets

-

Example data

- - -
    - -
  • - din32645
    Calibration data from DIN 32645
  • - -
  • - massart97ex1
    Calibration data from Massart et al. (1997), example 1
  • - -
-

Other

- - -
    - -
  • - chemCal-package
    Calibration functions for analytical chemistry -
  • - -
  • - massart97ex3
    Calibration data from Massart et al. (1997), example 3
  • - -
-
- -
-

Vignettes

- - -

Dependencies

-
    - - -
  • Suggests: MASS
  • - -
-

Authors

- - -
-
- - -
- - \ No newline at end of file diff --git a/inst/web/inverse.predict.html b/inst/web/inverse.predict.html deleted file mode 100644 index a513357..0000000 --- a/inst/web/inverse.predict.html +++ /dev/null @@ -1,202 +0,0 @@ - - - - -inverse.predict. chemCal 0.1-37 - - - - - - - - - - - - - - - - - -
-
- -
- -

Predict x from y for a linear calibration

- -
-
-

Usage

-
inverse.predict(object, newdata, ..., ws, alpha=0.05, var.s = "auto")
- -

Arguments

-
-
object
-
- A univariate model object of class lm or - rlm - with model formula y ~ x or y ~ x - 1. -
-
newdata
-
- A vector of observed y values for one sample. -
-
...
-
- Placeholder for further arguments that might be needed by - future implementations. -
-
ws
-
- The weight attributed to the sample. This argument is obligatory - if object has weights. -
-
alpha
-
- The error tolerance level for the confidence interval to be reported. -
-
var.s
-
- The estimated variance of the sample measurements. The default is to take - the residual standard error from the calibration and to adjust it - using ws, if applicable. This means that var.s - overrides ws. -
-
- -
-

Value

- -

- A list containing the predicted x value, its standard error and a - confidence interval. -

- -
- -
-

Description

- -

This function predicts x values using a univariate linear model that has been - generated for the purpose of calibrating a measurement method. Prediction - intervals are given at the specified confidence level. - The calculation method was taken from Massart et al. (1997). In particular, - Equations 8.26 and 8.28 were combined in order to yield a general treatment - of inverse prediction for univariate linear models, taking into account - weights that have been used to create the linear model, and at the same - time providing the possibility to specify a precision in sample measurements - differing from the precision in standard samples used for the calibration. - This is elaborated in the package vignette.

- -
- -
-

Note

- -

The function was validated with examples 7 and 8 from Massart et al. (1997).

- -
- -
-

References

- -

Massart, L.M, Vandenginste, B.G.M., Buydens, L.M.C., De Jong, S., Lewi, P.J., - Smeyers-Verbeke, J. (1997) Handbook of Chemometrics and Qualimetrics: Part A, - p. 200

- -
- -

Examples

-
# This is example 7 from Chapter 8 in Massart et al. (1997) -data(massart97ex1) -m <- lm(y ~ x, data = massart97ex1) -inverse.predict(m, 15) # 6.1 +- 4.9 -
-
$Prediction -[1] 6.09381 - -$`Standard Error` -[1] 1.767278 - -$Confidence -[1] 4.906751 - -$`Confidence Limits` -[1] 1.187059 11.000561 - -
-
inverse.predict(m, 90) # 43.9 +- 4.9 -
-
$Prediction -[1] 43.93983 - -$`Standard Error` -[1] 1.767747 - -$Confidence -[1] 4.908053 - -$`Confidence Limits` -[1] 39.03178 48.84788 - -
-
inverse.predict(m, rep(90,5)) # 43.9 +- 3.2 -
-
$Prediction -[1] 43.93983 - -$`Standard Error` -[1] 1.141204 - -$Confidence -[1] 3.168489 - -$`Confidence Limits` -[1] 40.77134 47.10832 - -
-
-
- - - -
-
- - -
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'show' : 'hide']() - } - - , show: function () { - var that = this - , e = $.Event('show') - - this.$element.trigger(e) - - if (this.isShown || e.isDefaultPrevented()) return - - $('body').addClass('modal-open') - - this.isShown = true - - escape.call(this) - backdrop.call(this, function () { - var transition = $.support.transition && that.$element.hasClass('fade') - - if (!that.$element.parent().length) { - that.$element.appendTo(document.body) //don't move modals dom position - } - - that.$element - .show() - - if (transition) { - that.$element[0].offsetWidth // force reflow - } - - that.$element.addClass('in') - - transition ? - that.$element.one($.support.transition.end, function () { that.$element.trigger('shown') }) : - that.$element.trigger('shown') - - }) - } - - , hide: function (e) { - e && e.preventDefault() - - var that = this - - e = $.Event('hide') - - this.$element.trigger(e) - - if (!this.isShown || e.isDefaultPrevented()) return - - this.isShown = false - - $('body').removeClass('modal-open') - - escape.call(this) - - this.$element.removeClass('in') - - $.support.transition && this.$element.hasClass('fade') ? - hideWithTransition.call(this) : - hideModal.call(this) - } - - } - - - /* MODAL PRIVATE METHODS - * ===================== */ - - function hideWithTransition() { - var that = this - , timeout = setTimeout(function () { - that.$element.off($.support.transition.end) - hideModal.call(that) - }, 500) - - this.$element.one($.support.transition.end, function () { - clearTimeout(timeout) - hideModal.call(that) - }) - } - - function hideModal(that) { - this.$element - .hide() - .trigger('hidden') - - backdrop.call(this) - } - - function backdrop(callback) { - var that = this - , animate = this.$element.hasClass('fade') ? 'fade' : '' - - if (this.isShown && this.options.backdrop) { - var doAnimate = $.support.transition && animate - - this.$backdrop = $('