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| -rw-r--r-- | README.md | 21 | ||||
| -rw-r--r-- | _pkgdown.yml | 22 | ||||
| -rw-r--r-- | docs/index.html | 13 | ||||
| -rw-r--r-- | docs/reference/index.html | 83 | ||||
| -rw-r--r-- | man/drfit-package.Rd | 34 |
5 files changed, 96 insertions, 77 deletions
@@ -1,8 +1,19 @@ ---- -title: Readme file for the drfit R package ---- +# 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-Static documentation of this R package can be found at -https://pkgdown.jrwb.de/drfit +A somewhat outdated package of basic and easy-to-use functions for +fitting dose-response curves to continuous dose-response data, calculating some +toxicological parameters and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) -} |