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authorJohannes Ranke <jranke@uni-bremen.de>2017-03-30 17:54:16 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2017-03-30 17:54:16 +0200
commitfec95dfbf0abe4175649e399eb1fcd698d482a9a (patch)
tree6d9a95ab2b129f5929d92a8851f96af4ec80b911 /docs
parent12a712a7b0cb0f755354f7a1f4e6e2d4c264fd13 (diff)
Add checkcontrols, updates, see ChangeLog
Diffstat (limited to 'docs')
-rw-r--r--docs/index.html10
-rw-r--r--docs/reference/antifoul.html29
-rw-r--r--docs/reference/drcfit.html11
3 files changed, 43 insertions, 7 deletions
diff --git a/docs/index.html b/docs/index.html
index 3ad6d4a..f6c1903 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -45,15 +45,15 @@
<div class="contents col-md-9">
A somewhat outdated package of basic and easy-to-use functions for
fitting dose-response curves to continuous dose-response data, calculating some
- (eco)toxicological parameters and plotting the results. Please consider using
+ 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 lognormal distribution
- (probit fit), of the logistic distribution (logit fit), of the weibull
- distribution (weibull fit) and a linear-logistic model ("linlogit" fit),
+ ('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 RODBC are included.
- As an alternative to the original fitting methods, the algorithms from the drc
+ dose-response data retrieved from a database accessed via 'RODBC' are included.
+ As an alternative to the original fitting methods, the algorithms from the 'drc'
package can be used.
</div>
diff --git a/docs/reference/antifoul.html b/docs/reference/antifoul.html
index 5a2b886..f5bc9fd 100644
--- a/docs/reference/antifoul.html
+++ b/docs/reference/antifoul.html
@@ -128,7 +128,34 @@
<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'>#&gt; <span class='message'></span>
-#&gt; <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#&gt; <span class='error'>Error in ED50["1:50", "Lower"]: Indizierung außerhalb der Grenzen</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>rantifoul.drc</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='output co'>#&gt; <span class='error'>Error in print(rantifoul.drc, digits = 5): Objekt 'rantifoul.drc' nicht gefunden</span></div></pre>
+#&gt; <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>rantifoul.drc</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='output co'>#&gt; Substance ndl n lld lhd mtype logED50 2.5% 97.5%
+#&gt; 1 TBT 38 135 -2.7093 2.3979 linlogit NA NA NA
+#&gt; 2 TBT 38 135 -2.7093 2.3979 probit -0.16436 -0.28178 -0.072022
+#&gt; 3 TBT 38 135 -2.7093 2.3979 logit -0.16012 -0.27782 -0.067603
+#&gt; 4 TBT 38 135 -2.7093 2.3979 weibull -0.13012 -0.23786 -0.043860
+#&gt; 5 Zn Pyrithion 27 81 -2.1072 2.0000 linlogit -0.41330 -0.54457 -0.312631
+#&gt; 6 Zn Pyrithion 27 81 -2.1072 2.0000 probit -0.39792 -0.52005 -0.302705
+#&gt; 7 Zn Pyrithion 27 81 -2.1072 2.0000 logit -0.40035 -0.52324 -0.304676
+#&gt; 8 Zn Pyrithion 27 81 -2.1072 2.0000 weibull -0.37351 -0.49792 -0.276917
+#&gt; unit sigma a b c ED50 ED50 2.5% ED50 97.5%
+#&gt; 1 microM 0.19264 0.71806 1.04061 -0.024169 NA NA NA
+#&gt; 2 microM 0.19286 0.68492 -0.64209 NA 0.68492 0.52267 0.84718
+#&gt; 3 microM 0.19199 0.69165 1.05007 NA 0.69165 0.52744 0.85585
+#&gt; 4 microM 0.18900 -0.13012 0.79816 NA 0.74111 0.57828 0.90394
+#&gt; 5 microM 0.22878 0.30926 1.74257 0.611358 0.38610 0.28538 0.48682
+#&gt; 6 microM 0.22866 0.40002 -1.04159 NA 0.40002 0.30196 0.49808
+#&gt; 7 microM 0.22802 0.39779 1.71015 NA 0.39779 0.29975 0.49582
+#&gt; 8 microM 0.23077 -0.37351 1.19152 NA 0.42315 0.31775 0.52855
+#&gt; EDx10 EDx10 2.5% EDx10 97.5%
+#&gt; 1 NA NA NA
+#&gt; 2 0.093074 0.040308 0.14584
+#&gt; 3 0.085338 0.035963 0.13471
+#&gt; 4 0.069958 0.026197 0.11372
+#&gt; 5 0.120238 0.043513 0.19696
+#&gt; 6 0.116878 0.048151 0.18561
+#&gt; 7 0.110068 0.043085 0.17705
+#&gt; 8 0.087066 0.017958 0.15617</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/drcfit.html b/docs/reference/drcfit.html
index ccf4641..75a168a 100644
--- a/docs/reference/drcfit.html
+++ b/docs/reference/drcfit.html
@@ -209,7 +209,16 @@
<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'>&lt;-</span> <span class='fu'>drcfit</span>(<span class='no'>antifoul</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'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#&gt; <span class='message'></span>
-#&gt; <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#&gt; <span class='error'>Error in ED50["1:50", "Lower"]: Indizierung außerhalb der Grenzen</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'>#&gt; <span class='error'>Error in format(r, digits = 2): Objekt 'r' nicht gefunden</span></div></pre>
+#&gt; <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>Zn Pyrithion: Fitting data...</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'>#&gt; Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma a
+#&gt; 1 TBT 38 135 -2.7 2.4 probit -0.16 -0.28 -0.072 microM 0.19 0.68
+#&gt; 2 Zn Pyrithion 27 81 -2.1 2.0 probit -0.40 -0.52 -0.303 microM 0.23 0.40
+#&gt; b ED50 ED50 2.5% ED50 97.5% EDx5 EDx5 2.5% EDx5 97.5% EDx10 EDx10 2.5%
+#&gt; 1 -0.64 0.68 0.52 0.85 0.053 0.015 0.091 0.093 0.040
+#&gt; 2 -1.04 0.40 0.30 0.50 0.082 0.023 0.142 0.117 0.048
+#&gt; EDx10 97.5% EDx20 EDx20 2.5% EDx20 97.5%
+#&gt; 1 0.15 0.18 0.11 0.26
+#&gt; 2 0.19 0.18 0.10 0.26</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>

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