diff options
Diffstat (limited to 'docs/reference')
| -rw-r--r-- | docs/reference/IM1xIPC81.html | 8 | ||||
| -rw-r--r-- | docs/reference/IM1xVibrio.html | 8 | ||||
| -rw-r--r-- | docs/reference/XY.html | 8 | ||||
| -rw-r--r-- | docs/reference/antifoul.html | 12 | ||||
| -rw-r--r-- | docs/reference/checkcontrols.html | 6 | ||||
| -rw-r--r-- | docs/reference/checkexperiment.html | 7 | ||||
| -rw-r--r-- | docs/reference/checksubstance.html | 7 | ||||
| -rw-r--r-- | docs/reference/drcfit.html | 19 | ||||
| -rw-r--r-- | docs/reference/drdata.html | 18 | ||||
| -rw-r--r-- | docs/reference/drfit-package.html | 6 | ||||
| -rw-r--r-- | docs/reference/drfit.html | 17 | ||||
| -rw-r--r-- | docs/reference/drplot.html | 9 | ||||
| -rw-r--r-- | docs/reference/index.html | 2 | ||||
| -rw-r--r-- | docs/reference/linlogitf.html | 3 | ||||
| -rw-r--r-- | docs/reference/pyrithione.html | 4 |
15 files changed, 60 insertions, 74 deletions
diff --git a/docs/reference/IM1xIPC81.html b/docs/reference/IM1xIPC81.html index d14afca..3ac5ef7 100644 --- a/docs/reference/IM1xIPC81.html +++ b/docs/reference/IM1xIPC81.html @@ -70,7 +70,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> </span> </div> @@ -126,7 +126,7 @@ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A dataframe containing the data as required for the - <code>drfit</code> function. An additional column contains + <code><a href='drfit.html'>drfit</a></code> function. An additional column contains the tested organism (name of the cell line).</p> <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> @@ -140,7 +140,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>rIM1xIPC81</span> <span class='kw'><-</span> <span class='fu'>drfit</span>(<span class='no'>IM1xIPC81</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fl'>10</span>)</div><div class='output co'>#> <span class='message'></span> + <pre class="examples"><div class='input'> <span class='no'>rIM1xIPC81</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>IM1xIPC81</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fl'>10</span>)</div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM13 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM14 BF4: Fitting data...</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM15 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> @@ -149,7 +149,7 @@ #> <span class='message'>IM18 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM19 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM1-10 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'> - <span class='no'>rIM1xIPC81.drc</span> <span class='kw'><-</span> <span class='fu'>drcfit</span>(<span class='no'>IM1xIPC81</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fl'>10</span>)</div><div class='output co'>#> <span class='message'></span> + <span class='no'>rIM1xIPC81.drc</span> <span class='kw'><-</span> <span class='fu'><a href='drcfit.html'>drcfit</a></span>(<span class='no'>IM1xIPC81</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fl'>10</span>)</div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM13 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM14 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM15 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> diff --git a/docs/reference/IM1xVibrio.html b/docs/reference/IM1xVibrio.html index 594efe1..0dde6b0 100644 --- a/docs/reference/IM1xVibrio.html +++ b/docs/reference/IM1xVibrio.html @@ -67,7 +67,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> </span> </div> @@ -119,7 +119,7 @@ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>A dataframe containing the data as required for the <code>drfit</code> + <p>A dataframe containing the data as required for the <code><a href='drfit.html'>drfit</a></code> function. Additional columns contain the species tested (luminescent bacteria Vibrio fischeri, <code>organism</code>), and a field specifying if the data is regarded valid (<code>ok</code>).</p> @@ -133,7 +133,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>rIM1xVibrio</span> <span class='kw'><-</span> <span class='fu'>drfit</span>(<span class='no'>IM1xVibrio</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <pre class="examples"><div class='input'> <span class='no'>rIM1xVibrio</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>IM1xVibrio</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM13 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM14 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> @@ -176,7 +176,7 @@ #> 14 0.7172 0.4132 5.2141 4.6652 5.801e+00 6.446e-01 1.394 #> 15 -0.1790 0.8019 0.6622 0.5534 7.876e-01 6.212e-02 0.140 #> 16 -0.1831 0.4816 0.6560 0.5470 7.843e-01 5.738e-02 0.141</div><div class='input'> - <span class='no'>rIM1xVibrio.drc</span> <span class='kw'><-</span> <span class='fu'>drcfit</span>(<span class='no'>IM1xVibrio</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='no'>rIM1xVibrio.drc</span> <span class='kw'><-</span> <span class='fu'><a href='drcfit.html'>drcfit</a></span>(<span class='no'>IM1xVibrio</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM13 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM14 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> diff --git a/docs/reference/XY.html b/docs/reference/XY.html index 2af3026..53770a3 100644 --- a/docs/reference/XY.html +++ b/docs/reference/XY.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> </span> </div> @@ -112,10 +112,6 @@ <p>A dataframe containing dose (concentration) and response data, as well as control values where the dose is zero.</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - - <p><a href='http://www.uft.uni-bremen.de/chemie'>http://www.uft.uni-bremen.de/chemie</a></p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> </div><span class='co'># NOT RUN {</span> @@ -127,8 +123,6 @@ <ul class="nav nav-pills nav-stacked"> <li><a href="#format">Format</a></li> - - <li><a href="#source">Source</a></li> <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/antifoul.html b/docs/reference/antifoul.html index d166ebd..7ea336a 100644 --- a/docs/reference/antifoul.html +++ b/docs/reference/antifoul.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> </span> </div> @@ -117,13 +117,9 @@ for TBT and Zink Pyrithione, respectively. Some additional columns from the database are also present.</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - - <p><a href='http://www.uft.uni-bremen.de/chemie'>http://www.uft.uni-bremen.de/chemie</a></p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>rantifoul.ED50</span> <span class='kw'><-</span> <span class='fu'>drfit</span>(<span class='no'>antifoul</span>, + <pre class="examples"><div class='input'><span class='no'>rantifoul.ED50</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>10</span>))</div><div class='output co'>#> <span class='message'></span> @@ -155,7 +151,7 @@ #> 6 0.116872 #> 7 0.110068 #> 8 0.121166</div><div class='input'> -<span class='no'>rantifoul.drc</span> <span class='kw'><-</span> <span class='fu'>drcfit</span>(<span class='no'>antifoul</span>, +<span class='no'>rantifoul.drc</span> <span class='kw'><-</span> <span class='fu'><a href='drcfit.html'>drcfit</a></span>(<span class='no'>antifoul</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>10</span>))</div><div class='output co'>#> <span class='message'></span> @@ -193,8 +189,6 @@ <ul class="nav nav-pills nav-stacked"> <li><a href="#format">Format</a></li> - - <li><a href="#source">Source</a></li> <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/checkcontrols.html b/docs/reference/checkcontrols.html index d3e4314..30baaed 100644 --- a/docs/reference/checkcontrols.html +++ b/docs/reference/checkcontrols.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> </span> </div> @@ -105,7 +105,8 @@ </div> - <pre class="usage"><span class='fu'>checkcontrols</span>(<span class='kw'>last</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, + <pre class="usage"><span class='fu'>checkcontrols</span>(<span class='kw'>last</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>db</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>, <span class='st'>"ecotox"</span>), <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"IPC-81"</span>, <span class='kw'>enzymetype</span> <span class='kw'>=</span> <span class='st'>"AChE"</span>, <span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"Vibrio fischeri"</span>, <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>qcc</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"R"</span>, <span class='st'>"xbar"</span>))</pre> @@ -180,7 +181,6 @@ Johannes Ranke <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - <a href='http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a> </div> </div> diff --git a/docs/reference/checkexperiment.html b/docs/reference/checkexperiment.html index 0712cd4..937b8dc 100644 --- a/docs/reference/checkexperiment.html +++ b/docs/reference/checkexperiment.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> </span> </div> @@ -105,8 +105,8 @@ </div> - <pre class="usage"><span class='fu'>checkplate</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>) - <span class='fu'>checkexperiment</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"ecotox"</span>, <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>)</pre> + <pre class="usage"><span class='fu'>checkplate</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>)) + <span class='fu'>checkexperiment</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"ecotox"</span>, <span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>), <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -153,7 +153,6 @@ Johannes Ranke <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - <a href='http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a> </div> </div> diff --git a/docs/reference/checksubstance.html b/docs/reference/checksubstance.html index 3f07df2..9f5899c 100644 --- a/docs/reference/checksubstance.html +++ b/docs/reference/checksubstance.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> </span> </div> @@ -105,7 +105,9 @@ </div> - <pre class="usage"><span class='fu'>checksubstance</span>(<span class='no'>substance</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>, + <pre class="usage"><span class='fu'>checksubstance</span>(<span class='no'>substance</span>, + <span class='kw'>db</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>, <span class='st'>"ecotox"</span>), + <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>enzymetype</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>whereClause</span> <span class='kw'>=</span> <span class='st'>"1"</span>, <span class='kw'>ok</span> <span class='kw'>=</span> <span class='st'>"%"</span>)</pre> @@ -187,7 +189,6 @@ Johannes Ranke <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - <a href='http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a> </div> </div> diff --git a/docs/reference/drcfit.html b/docs/reference/drcfit.html index d08b4b0..b4c299b 100644 --- a/docs/reference/drcfit.html +++ b/docs/reference/drcfit.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> </span> </div> @@ -120,7 +120,7 @@ used for the dose and a numeric vector “response” with the response values of the test system normalized between 0 and 1. Such a data frame can be easily obtained if a compliant RODBC data source is available for use in - conjunction with the function <code>drdata</code>.</p> + conjunction with the function <code><a href='drdata.html'>drdata</a></code>.</p> <p>If there is a column called “ok” and it is set to “no fit” in a specific line, then the corresponding data point will be excluded from the fitting procedure, although it will be plotted.</p></td> @@ -130,7 +130,7 @@ <td><p>A boolean defining if cumulative density curves of normal distributions are fitted against the decadic logarithm of the dose. Default ist TRUE. Note that the parameter definitions used in the model are different to the - ones used in <code>drfit</code>. Parameter e from <code>LN.2</code> is listed + ones used in <code><a href='drfit.html'>drfit</a></code>. Parameter e from <code>LN.2</code> is listed as a here, and parameter b from there is listed as b.</p></td> </tr> <tr> @@ -139,7 +139,7 @@ <code>plogis</code> are fitted to the decadic logarithm of the dose. Default is FALSE. Again the parameter definitions used in the model are different to the - ones used in <code>drfit</code>. Parameter e from <code>LL.2</code> is listed + ones used in <code><a href='drfit.html'>drfit</a></code>. Parameter e from <code>LL.2</code> is listed as a here, and parameter b from LL.2 is listed as b.</p></td> </tr> <tr> @@ -147,12 +147,12 @@ <td><p>A boolean defining if Weibull dose-response models (<code>W1.2</code> are fitted to the untransformed dose. Default is FALSE. Note that the results differ from the ones obtained with - <code>drfit</code>, due to a different model specification.</p></td> + <code><a href='drfit.html'>drfit</a></code>, due to a different model specification.</p></td> </tr> <tr> <th>linlogit</th> <td><p>A boolean defining if the linear-logistic function - <code>linlogitf</code> as defined by van Ewijk and Hoekstra 1993 is + <code><a href='linlogitf.html'>linlogitf</a></code> as defined by van Ewijk and Hoekstra 1993 is fitted to the data. Default is FALSE. Obtaining the ED50 (and EDx values in general) uses <code>ED</code> internally and does not always give a result.</p></td> @@ -212,7 +212,7 @@ parameters b from <code>BC.4</code>, <code>LN.2</code>, <code>LL.2</code> and <code>W1.2</code>, respectively. Note that the parameter definitions (and in the case of Weibull, the model - used) are different to the ones used in <code>drfit</code>.</p></dd> + used) are different to the ones used in <code><a href='drfit.html'>drfit</a></code>.</p></dd> <dt>c</dt><dd><p>Only the “linlogit” fit produces a third parameter <code>c</code>, which is the parameter f from the <code>BC.4</code> function.</p></dd> If the parameter showED50 was set to TRUE, the ED50 values and their @@ -231,8 +231,8 @@ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p>Further examples are given in help pages to the datasets - <code>antifoul</code>, <code>IM1xIPC81</code> and - <code>IM1xVibrio</code>.</p></div> + <code><a href='antifoul.html'>antifoul</a></code>, <code><a href='IM1xIPC81.html'>IM1xIPC81</a></code> and + <code><a href='IM1xVibrio.html'>IM1xVibrio</a></code>.</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -266,7 +266,6 @@ <h2>Author</h2> Johannes Ranke <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - <a href='http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a> The functionality of the drc package used under the hood in this function was written by Christian Ritz. diff --git a/docs/reference/drdata.html b/docs/reference/drdata.html index fc962be..438f32c 100644 --- a/docs/reference/drdata.html +++ b/docs/reference/drdata.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> </span> </div> @@ -103,8 +103,9 @@ </div> - <pre class="usage"><span class='fu'>drdata</span>(<span class='no'>substances</span>, <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"IPC-81"</span>, - <span class='kw'>enzymetype</span><span class='kw'>=</span><span class='st'>"AChE"</span>, <span class='kw'>organism</span><span class='kw'>=</span><span class='st'>"Vibrio fischeri"</span>, <span class='kw'>endpoint</span><span class='kw'>=</span><span class='st'>"Luminescence"</span>, + <pre class="usage"><span class='fu'>drdata</span>(<span class='no'>substances</span>, <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, + <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"IPC-81"</span>, <span class='kw'>enzymetype</span> <span class='kw'>=</span> <span class='st'>"AChE"</span>, <span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"Vibrio fischeri"</span>, + <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"Luminescence"</span>, <span class='kw'>whereClause</span> <span class='kw'>=</span> <span class='st'>"1"</span>, <span class='kw'>ok</span> <span class='kw'>=</span> <span class='st'>"'ok','no fit'"</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> @@ -201,10 +202,12 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'># Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81 -# cells -</div><span class='co'># NOT RUN {</span> -<span class='fu'>drdata</span>(<span class='fu'>c</span>(<span class='st'>"TBT"</span>,<span class='st'>"ZnPT2"</span>)) + <pre class="examples"><div class='input'> </div><span class='co'># NOT RUN {</span> + <span class='co'># Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81</span> + <span class='co'># cells</span> + <span class='fu'>drdata</span>(<span class='fu'>c</span>(<span class='st'>"TBT"</span>, <span class='st'>"ZnPT2"</span>)) + + <span class='co'># }</span></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -223,7 +226,6 @@ Johannes Ranke <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - <a href='http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a> </div> </div> diff --git a/docs/reference/drfit-package.html b/docs/reference/drfit-package.html index d2aa326..270cf91 100644 --- a/docs/reference/drfit-package.html +++ b/docs/reference/drfit-package.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> </span> </div> @@ -124,14 +124,14 @@ is its user-friendliness.</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>) -<span class='no'>r</span> <span class='kw'><-</span> <span class='fu'>drfit</span>(<span class='no'>antifoul</span>)</div><div class='output co'>#> <span class='message'></span> +<span class='no'>r</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</span>)</div><div class='output co'>#> <span class='message'></span> #> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'>format</span>(<span class='no'>r</span>,<span class='kw'>digits</span><span class='kw'>=</span><span class='fl'>2</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma a #> 1 TBT 38 135 -2.7 2.4 probit -0.16 -0.27 -0.056 microM 0.19 -0.16 #> 2 Zn Pyrithion 27 81 -2.1 2.0 probit -0.40 -0.51 -0.292 microM 0.23 -0.40 #> b #> 1 0.68 -#> 2 0.42</div><div class='input'><span class='fu'>drplot</span>(<span class='no'>r</span>,<span class='no'>antifoul</span>,<span class='kw'>overlay</span><span class='kw'>=</span><span class='fl'>TRUE</span>,<span class='kw'>bw</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='img'><img src='drfit-package-1.png' alt='' width='700' height='433' /></div></pre> +#> 2 0.42</div><div class='input'><span class='fu'><a href='drplot.html'>drplot</a></span>(<span class='no'>r</span>,<span class='no'>antifoul</span>,<span class='kw'>overlay</span><span class='kw'>=</span><span class='fl'>TRUE</span>,<span class='kw'>bw</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='img'><img src='drfit-package-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/drfit.html b/docs/reference/drfit.html index 4aa7935..93c2dae 100644 --- a/docs/reference/drfit.html +++ b/docs/reference/drfit.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> </span> </div> @@ -122,7 +122,7 @@ used for the dose and a numeric vector “response” with the response values of the test system normalized between 0 and 1. Such a data frame can be easily obtained if a compliant RODBC data source is available for use in - conjunction with the function <code>drdata</code>.</p> + conjunction with the function <code><a href='drdata.html'>drdata</a></code>.</p> <p>If there is a column called “ok” and it is set to “no fit” in a specific line, then the corresponding data point will be excluded from the fitting procedure, although it will be plotted.</p></td> @@ -156,7 +156,7 @@ <tr> <th>linlogit</th> <td><p>A boolean defining if the linear-logistic function - <code>linlogitf</code> as defined by van Ewijk and Hoekstra 1993 is + <code><a href='linlogitf.html'>linlogitf</a></code> as defined by van Ewijk and Hoekstra 1993 is fitted to the data. Default is FALSE.</p></td> </tr> <tr> @@ -249,13 +249,13 @@ parameter <code>a</code> coincides with the logED50. In the case of the “weibull” model, <code>a</code> is a location parameter.</p></dd> <dt>b</dt><dd><p>Parameter <code>b</code> in the case of the “linlogit” fit is the variable - b from the <code>linlogitf</code> function. In the case of “probit” + b from the <code><a href='linlogitf.html'>linlogitf</a></code> function. In the case of “probit” fit it is the standard deviation of the fitted normal distribution, in the case of the “logit” fit it is the <code>scale</code> parameter in the <code>plogis</code> function, and in the “weibull” fit it is the <code>shape</code> parameter of the fitted <code>pweibull</code> function.</p></dd> <dt>c</dt><dd><p>Only the “linlogit” fit produces a third parameter <code>c</code> which is - the variable f from the <code>linlogitf</code> function.</p></dd> + the variable f from the <code><a href='linlogitf.html'>linlogitf</a></code> function.</p></dd> If the parameter showED50 was set to TRUE, the ED50 values and their confidence intervals are also included on the original dose scale. @@ -271,10 +271,10 @@ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p>Further examples are given in help pages to the datasets - <code>antifoul</code>, <code>IM1xIPC81</code> and - <code>IM1xVibrio</code>. + <code><a href='antifoul.html'>antifoul</a></code>, <code><a href='IM1xIPC81.html'>IM1xIPC81</a></code> and + <code><a href='IM1xVibrio.html'>IM1xVibrio</a></code>. Since version 0.6.1 of this package, there is a drop-in replacement function - <code>drcfit</code> which internally uses the drc package and also gives + <code><a href='drcfit.html'>drcfit</a></code> which internally uses the drc package and also gives confidence intervals for EDx values via this package.</p></div> @@ -307,7 +307,6 @@ Johannes Ranke <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - <a href='http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a> </div> </div> diff --git a/docs/reference/drplot.html b/docs/reference/drplot.html index e5cbb22..24d69a8 100644 --- a/docs/reference/drplot.html +++ b/docs/reference/drplot.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> </span> </div> @@ -114,11 +114,11 @@ <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> <th>drresults</th> - <td><p>A data frame as returned from <code>drfit</code>.</p></td> + <td><p>A data frame as returned from <code><a href='drfit.html'>drfit</a></code>.</p></td> </tr> <tr> <th>data</th> - <td><p>A data frame as returned from <code>drdata</code>. The data frame has to + <td><p>A data frame as returned from <code><a href='drdata.html'>drdata</a></code>. The data frame has to contain at least a factor called "substance", a vector called "unit" containing the unit used for the dose, a column "response" with the response values of the test system normalized between 0 and 1, a column @@ -256,7 +256,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>) -<span class='no'>r</span> <span class='kw'><-</span> <span class='fu'>drfit</span>(<span class='no'>antifoul</span>)</div><div class='output co'>#> <span class='message'></span> +<span class='no'>r</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</span>)</div><div class='output co'>#> <span class='message'></span> #> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'>drplot</span>(<span class='no'>r</span>,<span class='no'>antifoul</span>)</div><div class='img'><img src='drplot-1.png' alt='' width='700' height='433' /></div><div class='img'><img src='drplot-2.png' alt='' width='700' height='433' /></div></pre> </div> @@ -276,7 +276,6 @@ Johannes Ranke <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - <a href='http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a> </div> </div> diff --git a/docs/reference/index.html b/docs/reference/index.html index 2b1f884..b05e223 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -58,7 +58,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> </span> </div> diff --git a/docs/reference/linlogitf.html b/docs/reference/linlogitf.html index 1dddf50..ba854f0 100644 --- a/docs/reference/linlogitf.html +++ b/docs/reference/linlogitf.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> </span> </div> @@ -157,7 +157,6 @@ Johannes Ranke <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - <a href='http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a> </div> </div> diff --git a/docs/reference/pyrithione.html b/docs/reference/pyrithione.html index 1488ecb..4e608d3 100644 --- a/docs/reference/pyrithione.html +++ b/docs/reference/pyrithione.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> </span> </div> @@ -111,7 +111,7 @@ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>A dataframe containing the data as required for the <code>drfit</code> + <p>A dataframe containing the data as required for the <code><a href='drfit.html'>drfit</a></code> function.</p> <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> |