From f4fcef8228ebd5a1a73bc6edc47b5efa259c2e20 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 23 Mar 2022 10:32:36 +0100
Subject: Use 'investr' conditionally in tests, updates

Most prominently, a README was added, giving a nice
overview for the people visiting the github page, the
package page on CRAN, or the online docs at pkgdown.jrwb.de.
The maintainer e-mail address was also updated.
---
 README.md | 141 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 137 insertions(+), 4 deletions(-)

(limited to 'README.md')

diff --git a/README.md b/README.md
index c60a2f8..2ad063e 100644
--- a/README.md
+++ b/README.md
@@ -1,10 +1,143 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.rmd. Please edit that file -->
+
+
+
 # chemCal - Calibration functions for analytical chemistry
 
 <!-- badges: start -->
 [![](https://www.r-pkg.org/badges/version/chemCal)](https://cran.r-project.org/package=chemCal)
-[![Build Status](https://travis-ci.com/jranke/chemCal.svg?branch=master)](https://travis-ci.com/jranke/chemCal)
-[![codecov](https://codecov.io/github/jranke/chemCal/branch/master/graphs/badge.svg)](https://codecov.io/github/jranke/chemCal) 
+[![Build Status](https://travis-ci.com/jranke/chemCal.svg?branch=master)](https://app.travis-ci.com/github/jranke/chemCal)
+[![codecov](https://codecov.io/github/jranke/chemCal/branch/master/graphs/badge.svg)](https://codecov.io/github/jranke/chemCal)
 <!-- badges: end -->
 
-Static documentation of this R package can be found at
-https://pkgdown.jrwb.de/chemCal
+## Overview
+
+chemCal is an R package providing some basic functions for conveniently working
+with linear calibration curves with one explanatory variable.
+
+## Installation
+
+From within [R][r-project], get the official chemCal release using
+
+
+```r
+install.packages("chemCal")
+```
+
+## Usage
+
+chemCal works with univariate linear models of class `lm`. Working with one of
+the datasets coming with chemCal, we can produce a calibration plot using the
+`calplot` function:
+
+### Plotting a calibration
+
+
+```r
+library(chemCal)
+m0 <- lm(y ~ x, data = massart97ex3)
+calplot(m0)
+```
+
+![](man/figures/README-calplot-1.png)<!-- -->
+
+### LOD and LOQ
+
+If you use unweighted regression, as in the above example, we can calculate a
+Limit Of Detection (LOD) from the calibration data.
+
+
+```r
+lod(m0)
+#> $x
+#> [1] 5.407085
+#> 
+#> $y
+#> [1] 13.63911
+```
+This is the minimum detectable value (German: Erfassungsgrenze), i.e. the
+value where the probability that the signal is not detected although the
+analyte is present is below a specified error tolerance beta (default is 0.05
+following the IUPAC recommendation).
+
+You can also calculate the decision limit (German: Nachweisgrenze), i.e.
+the value that is significantly different from the blank signal
+with an error tolerance alpha (default is 0.05, again following
+IUPAC recommendations) by setting beta to 0.5.
+
+
+```r
+lod(m0, beta = 0.5)
+#> $x
+#> [1] 2.720388
+#> 
+#> $y
+#> [1] 8.314841
+```
+
+Furthermore, you can calculate the Limit Of Quantification (LOQ), being
+defined as the value where the relative error of the quantification given the
+calibration model reaches a prespecified value (default is 1/3).
+
+
+```r
+loq(m0)
+#> $x
+#> [1] 9.627349
+#> 
+#> $y
+#> [1] 22.00246
+```
+
+### Confidence intervals for measured values
+
+Finally, you can get a confidence interval for the values
+measured using the calibration curve, i.e. for the inverse
+predictions using the function `inverse.predict`.
+
+
+```r
+inverse.predict(m0, 90)
+#> $Prediction
+#> [1] 43.93983
+#> 
+#> $`Standard Error`
+#> [1] 1.576985
+#> 
+#> $Confidence
+#> [1] 3.230307
+#> 
+#> $`Confidence Limits`
+#> [1] 40.70952 47.17014
+```
+
+If you have replicate measurements of the same sample,
+you can also give a vector of numbers.
+
+
+```r
+inverse.predict(m0, c(91, 89, 87, 93, 90))
+#> $Prediction
+#> [1] 43.93983
+#> 
+#> $`Standard Error`
+#> [1] 0.796884
+#> 
+#> $Confidence
+#> [1] 1.632343
+#> 
+#> $`Confidence Limits`
+#> [1] 42.30749 45.57217
+```
+
+## Reference
+
+You can use the R help system to view documentation, or you can
+have a look at the [online documentation][pd-site].
+
+[r-project]: https://r-project.org
+[pd-site]: https://pkgdown.jrwb.de/chemCal
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