Polish the static docs

5 files changed, 96 insertions, 77 deletions

diff --git a/README.md b/README.md
index 2430f79..fc01182 100644
--- a/README.md
+++ b/README.md
@@ -1,8 +1,19 @@
----
-title: Readme file for the drfit R package
----
+# drfit
 
 [![](https://www.r-pkg.org/badges/version/drfit)](https://cran.r-project.org/package=drfit)
 
-Static documentation of this R package can be found at
-https://pkgdown.jrwb.de/drfit
+A somewhat outdated package of basic and easy-to-use functions for
+fitting dose-response curves to continuous dose-response data, calculating some
+toxicological parameters and plotting the results. Please consider using
+the more powerful and actively developed 'drc' package.  
+
+Functions that are fitted are the cumulative density function of the log-normal
+distribution ('probit' fit), of the logistic distribution ('logit' fit), of the
+Weibull distribution ('weibull' fit) and a linear-logistic model ('linlogit'
+fit), derived from the latter, which is used to describe data showing
+stimulation at low doses (hormesis). In addition, functions checking, plotting
+and retrieving dose-response data retrieved from a database accessed via 'odbc'
+are included. As an alternative to the original fitting methods, the algorithms
+from the 'drc' package can be used.
+
+More details can be found in the [function referenc](reference/index.html).
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 0000000..804e836
--- /dev/null
+++ b/_pkgdown.yml
@@ -0,0 +1,22 @@
+reference:
+  - title: Main functions
+    contents:
+      - drfit
+      - drcfit
+      - drplot
+  - title: Get and check data from a drfit database
+    desc: These functions only work if you have such a database
+    contents:
+      - checkcontrols
+      - checkplate
+      - drdata
+  - title: Datasets and example evaluations
+    contents:
+      - antifoul
+      - IM1xIPC81
+      - IM1xVibrio
+      - pyrithione
+      - XY
+  - title: Helper functions
+    contents:
+      - linlogitf
diff --git a/docs/index.html b/docs/index.html
index 8b78e93..1b85668 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -70,15 +70,14 @@
 
       </header><div class="row">
   <div class="contents col-md-9">
+<div id="drfit" class="section level1">
+<div class="page-header"><h1 class="hasAnchor">
+<a href="#drfit" class="anchor"></a>drfit</h1></div>
 
-<hr>
-<div id="title-readme-file-for-the-drfit-r-package" class="section level2">
-<h2 class="hasAnchor">
-<a href="#title-readme-file-for-the-drfit-r-package" class="anchor"></a>title: Readme file for the drfit R package</h2>
-
-<p>Static documentation of this R package can be found at <a href="https://pkgdown.jrwb.de/drfit" class="uri">https://pkgdown.jrwb.de/drfit</a></p>
+<p>A somewhat outdated package of basic and easy-to-use functions for fitting dose-response curves to continuous dose-response data, calculating some toxicological parameters and plotting the results. Please consider using the more powerful and actively developed ‘drc’ package.</p>
+<p>Functions that are fitted are the cumulative density function of the log-normal distribution (‘probit’ fit), of the logistic distribution (‘logit’ fit), of the Weibull distribution (‘weibull’ fit) and a linear-logistic model (‘linlogit’ fit), derived from the latter, which is used to describe data showing stimulation at low doses (hormesis). In addition, functions checking, plotting and retrieving dose-response data retrieved from a database accessed via ‘odbc’ are included. As an alternative to the original fitting methods, the algorithms from the ‘drc’ package can be used.</p>
+<p>More details can be found in the <a href="reference/index.html">function referenc</a>.</p>
 </div>
-
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 7203c94..cbd742c 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -112,35 +112,37 @@
     <tbody>
       <tr>
         <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
+          <h2 id="section-main-functions" class="hasAnchor"><a href="#section-main-functions" class="anchor"></a>Main functions</h2>
           <p class="section-desc"></p>
         </th>
       </tr>
       <tr>
         
         <td>
-          <p><code><a href="IM1xIPC81.html">IM1xIPC81</a></code> </p>
-        </td>
-        <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="IM1xVibrio.html">IM1xVibrio</a></code> </p>
+          <p><code><a href="drfit.html">drfit()</a></code> </p>
         </td>
-        <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri</p></td>
+        <td><p>Fit dose-response models</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="XY.html">XY</a></code> </p>
+          <p><code><a href="drcfit.html">drcfit()</a></code> </p>
         </td>
-        <td><p>Dose-Response data for two substances X and Y</p></td>
+        <td><p>Fit dose-response models using the drc package</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="antifoul.html">antifoul</a></code> </p>
+          <p><code><a href="drplot.html">drplot()</a></code> </p>
         </td>
-        <td><p>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</p></td>
-      </tr><tr>
+        <td><p>Plot dose-response models</p></td>
+      </tr>
+    </tbody><tbody>
+      <tr>
+        <th colspan="2">
+          <h2 id="section-get-and-check-data-from-a-drfit-database" class="hasAnchor"><a href="#section-get-and-check-data-from-a-drfit-database" class="anchor"></a>Get and check data from a drfit database</h2>
+          <p class="section-desc"><p>These functions only work if you have such a database</p></p>
+        </th>
+      </tr>
+      <tr>
         
         <td>
           <p><code><a href="checkcontrols.html">checkcontrols()</a></code> </p>
@@ -155,45 +157,61 @@
       </tr><tr>
         
         <td>
-          <p><code><a href="drcfit.html">drcfit()</a></code> </p>
+          <p><code><a href="drdata.html">drdata()</a></code> </p>
         </td>
-        <td><p>Fit dose-response models using the drc package</p></td>
-      </tr><tr>
+        <td><p>Get dose-response data via RODBC</p></td>
+      </tr>
+    </tbody><tbody>
+      <tr>
+        <th colspan="2">
+          <h2 id="section-datasets-and-example-evaluations" class="hasAnchor"><a href="#section-datasets-and-example-evaluations" class="anchor"></a>Datasets and example evaluations</h2>
+          <p class="section-desc"></p>
+        </th>
+      </tr>
+      <tr>
         
         <td>
-          <p><code><a href="drdata.html">drdata()</a></code> </p>
+          <p><code><a href="antifoul.html">antifoul</a></code> </p>
         </td>
-        <td><p>Get dose-response data via RODBC</p></td>
+        <td><p>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="drfit-package.html">drfit-package</a></code> </p>
+          <p><code><a href="IM1xIPC81.html">IM1xIPC81</a></code> </p>
         </td>
-        <td><p>Dose-response data evaluation</p></td>
+        <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="drfit.html">drfit()</a></code> </p>
+          <p><code><a href="IM1xVibrio.html">IM1xVibrio</a></code> </p>
         </td>
-        <td><p>Fit dose-response models</p></td>
+        <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="drplot.html">drplot()</a></code> </p>
+          <p><code><a href="pyrithione.html">pyrithione</a></code> </p>
         </td>
-        <td><p>Plot dose-response models</p></td>
+        <td><p>Cytotoxicity data for different pyrithionates and related species</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="linlogitf.html">linlogitf()</a></code> </p>
+          <p><code><a href="XY.html">XY</a></code> </p>
         </td>
-        <td><p>Linear-logistic function</p></td>
-      </tr><tr>
+        <td><p>Dose-Response data for two substances X and Y</p></td>
+      </tr>
+    </tbody><tbody>
+      <tr>
+        <th colspan="2">
+          <h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2>
+          <p class="section-desc"></p>
+        </th>
+      </tr>
+      <tr>
         
         <td>
-          <p><code><a href="pyrithione.html">pyrithione</a></code> </p>
+          <p><code><a href="linlogitf.html">linlogitf()</a></code> </p>
         </td>
-        <td><p>Cytotoxicity data for different pyrithionates and related species</p></td>
+        <td><p>Linear-logistic function</p></td>
       </tr>
     </tbody>
     </table>
@@ -202,7 +220,10 @@
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
     <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
+      <li><a href="#section-main-functions">Main functions</a></li>
+      <li><a href="#section-get-and-check-data-from-a-drfit-database">Get and check data from a drfit database</a></li>
+      <li><a href="#section-datasets-and-example-evaluations">Datasets and example evaluations</a></li>
+      <li><a href="#section-helper-functions">Helper functions</a></li>
     </ul>
   </div>
 </div>
diff --git a/man/drfit-package.Rd b/man/drfit-package.Rd
deleted file mode 100644
index 06a147f..0000000
--- a/man/drfit-package.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-\name{drfit-package}
-\alias{drfit-package}
-\docType{package}
-\title{
-Dose-response data evaluation
-}
-\description{
-See \url{../DESCRIPTION}
-}
-\details{
-There is an introductory article located in \url{../doc/drfit-Rnews.pdf},
-which will be published in the R News special edition on the use
-of R for chemists.
-}
-\author{
-Author and Maintainer: Johannes Ranke <jranke@uni-bremen.de>
-}
-\note{There is a demo for each dataset that can be accessed by
-  \code{demo(dataset)}}
-\keyword{ package }
-\keyword{ models }
-\keyword{ regression }
-\keyword{ nonlinear }
-\seealso{
-On CRAN, there is another, more statistically sophisticated package with
-similar functionality called \code{drc}. I think the advantage of my package
-is its user-friendliness.
-}
-\examples{
-data(antifoul)
-r <- drfit(antifoul)
-format(r,digits=2)
-drplot(r,antifoul,overlay=TRUE,bw=FALSE)
-}