Further improvement to checkcontrols()

Static documentation rebuilt by pkgdown::build_site()

16 files changed, 924 insertions, 60 deletions

diff --git a/R/checkcontrols.R b/R/checkcontrols.R
index df9a2f9..d996d18 100644
--- a/R/checkcontrols.R
+++ b/R/checkcontrols.R
@@ -1,5 +1,6 @@
 if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "conc"))
 checkcontrols <- function(last = 10, id = NULL, db = "cytotox",
+                          celltype = "IPC-81", enzymetype = "AChE",
                           organism = "Vibrio fischeri",
                           endpoint = "%", qcc = c("R", "xbar"))
 {
@@ -14,8 +15,17 @@ checkcontrols <- function(last = 10, id = NULL, db = "cytotox",
 
     if (db %in% c("cytotox","enzymes")) {
         if (is.null(id[1])) {
-            platequery <- paste("SELECT plate FROM controls",
-                "GROUP BY plate ORDER BY plate DESC LIMIT", last)
+            platequery <- "SELECT plate FROM"
+            if (db == "cytotox") {
+                platequery <- paste0(platequery, " cytotox WHERE celltype like
+                                     '", celltype, "'")
+            }
+            if (db == "enzymes") {
+                platequery <- paste0(platequery, " enzymes WHERE enzyme like
+                                     '", enzymetype, "'")
+            }
+                platequery <- paste(platequery,
+                    "GROUP BY plate ORDER BY plate DESC LIMIT", last)
             plates <- RODBC::sqlQuery(channel, platequery)$plate
         } else {
             plates <- id
@@ -25,26 +35,39 @@ checkcontrols <- function(last = 10, id = NULL, db = "cytotox",
         controldata <- RODBC::sqlQuery(channel,controlquery)
     } else {
         if (is.null(id[1])) {
-            lastquery = paste0("SELECT experiment FROM ecotox ",
-                "WHERE type LIKE '", endpoint, "' ",
+            lastquery = paste0("SELECT experiment, type FROM ecotox ",
+                "WHERE organism LIKE '", organism, "'",
+                "AND type LIKE '", endpoint, "' ",
                 "GROUP BY experiment ORDER BY experiment DESC LIMIT ", last)
             res <- RODBC::sqlQuery(channel, lastquery)
             if (nrow(res) == 0) {
                 stop("No results for endpoint", endpoint)
             } else {
+                if (nlevels(res$type) > 1) {
+                    stop("Found more than one endpoint type:\n",
+                         paste(levels(res$type), collapse = ", "), "\n",
+                         "Please specify an endpoint in your call to checkcontrols()")
+                }
                 experiments <- res$experiment
             }
         } else {
             experiments <- id
         }
-        expquery <- paste("SELECT ",
-            "experimentator, substance, organism, conc, unit, response, ",
+        expquery <- paste0("SELECT ",
+            "experimentator, experiment, substance, organism, type, conc, unit, raw_response, ",
             "performed, ok ",
             "FROM ecotox ",
             "WHERE experiment IN (", paste(experiments, collapse = ", "), ") ",
             "AND organism LIKE '", organism, "' ",
-            "AND type LIKE '", endpoint, "'", sep = "")
+            "AND type LIKE '", endpoint, "'")
         expdata <- RODBC::sqlQuery(channel, expquery)
+        if (nlevels(expdata$type) > 1) {
+            stop("Found more than one endpoint type:\n",
+                 paste(levels(expdata$type), collapse = ", "), "\n",
+                 "Please specify an endpoint in your call to checkcontrols()")
+        }
+        # Use the raw response for QA
+        expdata$response <- expdata$raw_response
     }
 
     RODBC::odbcClose(channel)
@@ -76,13 +99,17 @@ checkcontrols <- function(last = 10, id = NULL, db = "cytotox",
                                               QA["Control (conc = 0)", 2],2)
     }
 
+    # The report
+    cat("\nDatabase", db, "\n")
+
     if (db == "ecotox") {
-        endpoint_string = if(endpoint == "%") "any endpoint" else paste("endpoint", endpoint)
-        cat("\nExperiments ", paste(experiments, collapse = ", "),
-            " from database ecotox for ", endpoint_string, " for ", organism, ":\n\n", sep = "")
+        cat("Organism", organism, "\n")
+        cat("Endpoint", unique(expdata$type), "\n")
+        cat("\nExperiments ", paste(experiments, collapse = ", "), "\n\n")
     } else {
-        cat("\nPlates ", paste(plates, collapse = ", "),
-            " from database ", db, ":\n\n", sep = "")
+        if (db == "cytotox") cat ("Cell type", celltype, "\n")
+        if (db == "enzymes") cat ("Enzyme type", enzymetype, "\n")
+        cat("\nPlates", paste(plates, collapse = ", "), "\n\n")
     }
     print(QA)
 
@@ -90,9 +117,17 @@ checkcontrols <- function(last = 10, id = NULL, db = "cytotox",
         op <- par(ask=TRUE)
         on.exit(par(op))
         requireNamespace("reshape2")
-        controls_molten <- melt(controls[c("plate", "location", "response")],
-                                id = c("plate", "location"))
-        controls_wide <- acast(controls_molten, formula = plate ~ location)
+        if (db == "ecotox") {
+            controls$row <- rownames(controls)
+            controls_molten <- melt(controls[c("experiment", "row", "response")],
+                                    id = c("experiment", "row"))
+            controls_wide <- acast(controls_molten, formula = experiment ~ row)
+
+        } else {
+            controls_molten <- melt(controls[c("plate", "location", "response")],
+                                    id = c("plate", "location"))
+            controls_wide <- acast(controls_molten, formula = plate ~ location)
+        }
         if ("R" %in% qcc) {
             qcc(controls_wide, type = "R", nsigmas = 3,
                 title = "Range chart",
diff --git a/check.log b/check.log
index 5d1e47c..2ad8764 100644
--- a/check.log
+++ b/check.log
@@ -2,12 +2,9 @@
 * using R version 3.3.3 (2017-03-06)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
-* using option ‘--as-cran’
 * checking for file ‘drfit/DESCRIPTION’ ... OK
 * this is package ‘drfit’ version ‘0.7.1’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
-Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
 * checking package namespace information ... OK
 * checking package dependencies ... OK
 * checking if this is a source package ... OK
@@ -32,7 +29,6 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
 * checking whether the namespace can be loaded with stated dependencies ... OK
 * checking whether the namespace can be unloaded cleanly ... OK
 * checking loading without being on the library search path ... OK
-* checking use of S3 registration ... OK
 * checking dependencies in R code ... OK
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
@@ -40,7 +36,6 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
 * checking R code for possible problems ... OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
-* checking Rd line widths ... OK
 * checking Rd cross-references ... OK
 * checking for missing documentation entries ... OK
 * checking for code/documentation mismatches ... OK
diff --git a/docs/index.html b/docs/index.html
index f6c1903..6360f04 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -47,7 +47,7 @@
   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 lognormal distribution
+  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
diff --git a/docs/reference/IM1xIPC81.html b/docs/reference/IM1xIPC81.html
new file mode 100644
index 0000000..6ab98e7
--- /dev/null
+++ b/docs/reference/IM1xIPC81.html
@@ -0,0 +1,196 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
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+<title>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells — IM1xIPC81 • drfit</title>
+
+<!-- jquery -->
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+    <div id="navbar" class="navbar-collapse collapse">
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+  <a href="../reference/index.html">Reference</a>
+</li>
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+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells</h1>
+    </div>
+
+    
+    <p>This is the raw data documenting the influence of the alkyl
+  chain length in 3 position on the toxicity to the
+  promyelocytic leukemia rat cell line IPC-81. The substances
+  are named according to the UFT naming scheme of these
+  substances. IM13 BF4 means 1-methyl-3-propylimidazolium
+  tetrafluoroborate, IM14 BF4 means
+  1-methyl-3-butylimidazolium tetrafluoroborate and IM1-10
+  BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate.
+  This is a subset (only the BF4 anion) of the data
+  shown in Figure 3 in Ranke et al. (2004).</p>
+    
+
+    <pre><span class='fu'>data</span>(<span class='no'>IM1xIPC81</span>)</pre>
+        
+    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+    <p>A dataframe containing the data as required for the
+  <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>
+
+    <p>Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J,
+  Hoffmann J, Ondruschka B, Filser J, Jastorff B (2004)
+  Biological effects of imidazolium ionic liquids with varying
+  chain lenghts in acute Vibrio fischeri and WST-1 cell
+  viability assays. Ecotoxicology and Environmental Safety
+  58(3) 396-404</p>
+    
+
+    <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'>&lt;-</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'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM13 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM14 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM15 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM16 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM17 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM18 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM19 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM1-10 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='input'>
+  <span class='no'>rIM1xIPC81.drc</span> <span class='kw'>&lt;-</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'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM13 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM14 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM15 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM16 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM17 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM18 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM19 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM1-10 BF4: Fitting data...</span></div><div class='input'>
+  <span class='fu'>print</span>(<span class='no'>rIM1xIPC81</span>,<span class='kw'>digits</span><span class='kw'>=</span><span class='fl'>4</span>)</div><div class='output co'>#&gt;    Substance ndl   n     lld   lhd    mtype logED50  2.5%  97.5%   unit  sigma
+#&gt; 1   IM13 BF4   9  81  0.5918 3.000 inactive      NA    NA     NA microM     NA
+#&gt; 2   IM14 BF4  20 216 -0.0103 3.176   no fit      NA    NA     NA microM     NA
+#&gt; 3   IM15 BF4   9 135  0.5918 3.000 inactive      NA    NA     NA microM     NA
+#&gt; 4   IM16 BF4   9 108  0.5918 3.000 inactive      NA    NA     NA microM     NA
+#&gt; 5   IM17 BF4   9  81  0.5918 3.000 linlogit  2.5786 2.506 2.6617 microM 0.2376
+#&gt; 6   IM18 BF4   9 135  0.5918 3.000 linlogit  1.6806 1.623 1.7419 microM 0.2325
+#&gt; 7   IM19 BF4   9  81  0.5918 3.000 linlogit  1.6496 1.598 1.7031 microM 0.1453
+#&gt; 8 IM1-10 BF4  11 162 -0.0103 3.000 linlogit  0.7697 0.687 0.8544 microM 0.2988
+#&gt;        a     b       c    ED50 ED50 2.5% ED50 97.5%   EDx10
+#&gt; 1     NA    NA      NA      NA        NA         NA      NA
+#&gt; 2     NA    NA      NA      NA        NA         NA      NA
+#&gt; 3     NA    NA      NA      NA        NA         NA      NA
+#&gt; 4     NA    NA      NA      NA        NA         NA      NA
+#&gt; 5 2.5786 2.300 0.01468 378.941   320.424    458.918 230.782
+#&gt; 6 1.6806 2.237 0.05719  47.930    41.973     55.194  27.367
+#&gt; 7 1.6496 1.977 0.10956  44.628    39.671     50.483  23.031
+#&gt; 8 0.7697 1.936 0.45809   5.884     4.864      7.152   2.835</div><div class='input'>  <span class='fu'>print</span>(<span class='no'>rIM1xIPC81.drc</span>,<span class='kw'>digits</span><span class='kw'>=</span><span class='fl'>4</span>)</div><div class='output co'>#&gt;    Substance ndl   n     lld   lhd    mtype logED50   2.5%  97.5%   unit  sigma
+#&gt; 1   IM13 BF4   9  81  0.5918 3.000 inactive      NA     NA     NA microM     NA
+#&gt; 2   IM14 BF4  20 216 -0.0103 3.176 linlogit      NA     NA     NA microM 0.1529
+#&gt; 3   IM15 BF4   9 135  0.5918 3.000 inactive      NA     NA     NA microM     NA
+#&gt; 4   IM16 BF4   9 108  0.5918 3.000 inactive      NA     NA     NA microM     NA
+#&gt; 5   IM17 BF4   9  81  0.5918 3.000 linlogit  2.5786 2.4935 2.6497 microM 0.2376
+#&gt; 6   IM18 BF4   9 135  0.5918 3.000 linlogit  1.6806 1.6168 1.7362 microM 0.2325
+#&gt; 7   IM19 BF4   9  81  0.5918 3.000 linlogit  1.6496 1.5940 1.6990 microM 0.1453
+#&gt; 8 IM1-10 BF4  11 162 -0.0103 3.000 linlogit  0.7697 0.6774 0.8458 microM 0.2988
+#&gt;           a      b          c    ED50 ED50 2.5% ED50 97.5%   EDx10 EDx10 2.5%
+#&gt; 1        NA     NA         NA      NA        NA         NA      NA         NA
+#&gt; 2 5.390e+15 0.3148 -0.0001736      NA        NA         NA      NA         NA
+#&gt; 3        NA     NA         NA      NA        NA         NA      NA         NA
+#&gt; 4        NA     NA         NA      NA        NA         NA      NA         NA
+#&gt; 5 1.281e+02 2.3001  0.0146821 378.964   311.555    446.372 230.790    202.915
+#&gt; 6 2.079e+01 2.2373  0.0571925  47.930    41.382     54.478  27.367     23.809
+#&gt; 7 1.342e+01 1.9773  0.1094542  44.630    39.260     50.000  23.036     20.614
+#&gt; 8 2.258e+00 1.9362  0.4580784   5.884     4.758      7.011   2.835      2.181
+#&gt;   EDx10 97.5%
+#&gt; 1          NA
+#&gt; 2          NA
+#&gt; 3          NA
+#&gt; 4          NA
+#&gt; 5     258.665
+#&gt; 6      30.925
+#&gt; 7      25.459
+#&gt; 8       3.489</div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <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>
+
+  </div>
+</div>
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+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
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diff --git a/docs/reference/IM1xVibrio.html b/docs/reference/IM1xVibrio.html
new file mode 100644
index 0000000..79c3d95
--- /dev/null
+++ b/docs/reference/IM1xVibrio.html
@@ -0,0 +1,233 @@
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+  <a href="../reference/index.html">Reference</a>
+</li>
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+        
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+    <h1>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri</h1>
+    </div>
+
+    
+    <p>This is the raw data documenting the influence of the alkyl chain length in 3
+  position on the toxicity to the marine luminescent bacteria <em>V.
+  fischeri</em>. The substances are named according to the UFT naming scheme of
+  these substances.
+  IM13 BF4 means 1-methyl-3-propylimidazolium tetrafluoroborate,
+  IM14 BF4 means 1-methyl-3-butylimidazolium tetrafluoroborate and
+  IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate.</p>
+    
+
+    <pre><span class='fu'>data</span>(<span class='no'>IM1xVibrio</span>)</pre>
+        
+    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+    <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>
+    
+    <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+    <p>Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J,
+  Ondruschka B, Filser J, Jastorff B (2004) Biological effects of imidazolium
+  ionic liquids with varying chain lenghts in acute Vibrio fischeri and WST-1
+  cell viability assays. Ecotoxicology and Environmental Safety 58(3) 396-404</p>
+    
+
+    <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'>&lt;-</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'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM13 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM14 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM15 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM16 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM17 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM18 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM19 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM1-10 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='input'>  <span class='fu'>print</span>(<span class='no'>rIM1xVibrio</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='output co'>#&gt;     Substance ndl  n    lld   lhd  mtype logED50    2.5%   97.5%   unit   sigma
+#&gt; 1    IM13 BF4  13 22 -5.301 4.699 probit  3.9399  3.8636  4.0160 microM 0.06303
+#&gt; 2    IM13 BF4  13 22 -5.301 4.699  logit  3.9461  3.8708  4.0211 microM 0.06188
+#&gt; 3    IM14 BF4  12 57 -4.301 4.699 probit  3.5442  3.5030  3.5855 microM 0.05905
+#&gt; 4    IM14 BF4  12 57 -4.301 4.699  logit  3.5465  3.5044  3.5885 microM 0.06030
+#&gt; 5    IM15 BF4   7 20 -0.301 4.699 probit  3.1398  3.1136  3.1662 microM 0.02695
+#&gt; 6    IM15 BF4   7 20 -0.301 4.699  logit  3.1387  3.1118  3.1659 microM 0.02723
+#&gt; 7    IM16 BF4  13 30 -4.301 4.699 probit  3.1804  3.1436  3.2176 microM 0.04514
+#&gt; 8    IM16 BF4  13 30 -4.301 4.699  logit  3.1814  3.1440  3.2190 microM 0.04553
+#&gt; 9    IM17 BF4  10 20 -1.301 4.699 probit  2.4317  2.3681  2.4951 microM 0.04773
+#&gt; 10   IM17 BF4  10 20 -1.301 4.699  logit  2.4353  2.3672  2.5026 microM 0.05050
+#&gt; 11   IM18 BF4  10 17 -2.301 2.699 probit  1.4015  1.3147  1.4881 microM 0.05611
+#&gt; 12   IM18 BF4  10 17 -2.301 2.699  logit  1.4051  1.3129  1.4966 microM 0.05898
+#&gt; 13   IM19 BF4  13 22 -5.301 2.699 probit  0.7158  0.6704  0.7592 microM 0.02956
+#&gt; 14   IM19 BF4  13 22 -5.301 2.699  logit  0.7172  0.6689  0.7635 microM 0.03210
+#&gt; 15 IM1-10 BF4  11 20 -6.301 2.699 probit -0.1790 -0.2569 -0.1037 microM 0.04099
+#&gt; 16 IM1-10 BF4  11 20 -6.301 2.699  logit -0.1831 -0.2620 -0.1055 microM 0.04192
+#&gt;          a      b      ED50 ED50 2.5% ED50 97.5%     EDx10    EDx20
+#&gt; 1   3.9399 0.5763 8707.8956 7305.0279  1.038e+04 1.590e+03 2850.222
+#&gt; 2   3.9461 0.3426 8832.9407 7426.2282  1.050e+04 1.561e+03 2959.147
+#&gt; 3   3.5442 0.6561 3501.1558 3184.3196  3.851e+03 5.051e+02  981.759
+#&gt; 4   3.5465 0.3911 3519.5779 3194.6808  3.877e+03 4.867e+02 1010.014
+#&gt; 5   3.1398 0.5527 1379.9037 1298.9533  1.466e+03 2.701e+02  472.823
+#&gt; 6   3.1387 0.3347 1376.4086 1293.7152  1.465e+03 2.532e+02  472.911
+#&gt; 7   3.1804 0.4882 1515.0421 1391.8150  1.650e+03 3.588e+02  588.292
+#&gt; 8   3.1814 0.2957 1518.4650 1393.2665  1.656e+03 3.401e+02  590.840
+#&gt; 9   2.4317 0.6387  270.2279  233.3814  3.127e+02 4.105e+01   78.382
+#&gt; 10  2.4353 0.3810  272.4409  232.9287  3.182e+02 3.965e+01   80.754
+#&gt; 11  1.4015 0.8009   25.2069   20.6383  3.077e+01 2.372e+00    5.340
+#&gt; 12  1.4051 0.4816   25.4135   20.5545  3.138e+01 2.222e+00    5.463
+#&gt; 13  0.7158 0.6969    5.1975    4.6814  5.744e+00 6.647e-01    1.347
+#&gt; 14  0.7172 0.4132    5.2141    4.6652  5.801e+00 6.446e-01    1.394
+#&gt; 15 -0.1790 0.8019    0.6622    0.5534  7.876e-01 6.212e-02    0.140
+#&gt; 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'>&lt;-</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'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM13 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM14 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM15 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM16 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM17 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM18 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM19 BF4: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>IM1-10 BF4: Fitting data...</span></div><div class='input'>  <span class='fu'>print</span>(<span class='no'>rIM1xVibrio.drc</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='output co'>#&gt;     Substance ndl  n    lld   lhd  mtype logED50    2.5%   97.5%   unit   sigma
+#&gt; 1    IM13 BF4  13 22 -5.301 4.699 probit  3.9399  3.8563  4.0100 microM 0.06303
+#&gt; 2    IM13 BF4  13 22 -5.301 4.699  logit  3.9461  3.8637  4.0153 microM 0.06188
+#&gt; 3    IM14 BF4  12 57 -4.301 4.699 probit  3.5442  3.5009  3.5836 microM 0.05905
+#&gt; 4    IM14 BF4  12 57 -4.301 4.699  logit  3.5465  3.5023  3.5866 microM 0.06030
+#&gt; 5    IM15 BF4   7 20 -0.301 4.699 probit  3.1398  3.1127  3.1654 microM 0.02695
+#&gt; 6    IM15 BF4   7 20 -0.301 4.699  logit  3.1387  3.1109  3.1649 microM 0.02723
+#&gt; 7    IM16 BF4  13 30 -4.301 4.699 probit  3.1804  3.1419  3.2158 microM 0.04514
+#&gt; 8    IM16 BF4  13 30 -4.301 4.699  logit  3.1814  3.1424  3.2172 microM 0.04553
+#&gt; 9    IM17 BF4  10 20 -1.301 4.699 probit  2.4317  2.3632  2.4909 microM 0.04773
+#&gt; 10   IM17 BF4  10 20 -1.301 4.699  logit  2.4353  2.3618  2.4981 microM 0.05050
+#&gt; 11   IM18 BF4  10 17 -2.301 2.699 probit  1.4015  1.3052  1.4803 microM 0.05611
+#&gt; 12   IM18 BF4  10 17 -2.301 2.699  logit  1.4051  1.3023  1.4881 microM 0.05898
+#&gt; 13   IM19 BF4  13 22 -5.301 2.699 probit  0.7158  0.6690  0.7580 microM 0.02956
+#&gt; 14   IM19 BF4  13 22 -5.301 2.699  logit  0.7172  0.6672  0.7620 microM 0.03210
+#&gt; 15 IM1-10 BF4  11 20 -6.301 2.699 probit -0.1790 -0.2628 -0.1088 microM 0.04099
+#&gt; 16 IM1-10 BF4  11 20 -6.301 2.699  logit -0.1831 -0.2690 -0.1114 microM 0.04192
+#&gt;            a       b      ED50 ED50 2.5% ED50 97.5%     EDx10 EDx10 2.5%
+#&gt; 1  8707.5571 -0.7536 8707.5571 7183.0127  1.023e+04 1.590e+03  968.72501
+#&gt; 2  8832.8773  1.2676 8832.8773 7306.8669  1.036e+04 1.561e+03  925.39582
+#&gt; 3  3501.1967 -0.6619 3501.1967 3168.9639  3.833e+03 5.051e+02  395.26341
+#&gt; 4  3519.5773  1.1105 3519.5773 3179.2923  3.860e+03 4.866e+02  371.84710
+#&gt; 5  1379.9019 -0.7858 1379.9019 1296.3162  1.463e+03 2.701e+02  233.25320
+#&gt; 6  1376.4086  1.2976 1376.4086 1290.8397  1.462e+03 2.531e+02  215.79719
+#&gt; 7  1515.0427 -0.8896 1515.0427 1386.3308  1.644e+03 3.588e+02  283.79434
+#&gt; 8  1518.4644  1.4686 1518.4644 1387.9173  1.649e+03 3.401e+02  262.20564
+#&gt; 9   270.2279 -0.6800  270.2279  230.7905  3.097e+02 4.105e+01   27.78507
+#&gt; 10  272.4526  1.1401  272.4526  230.0588  3.148e+02 3.966e+01   25.34948
+#&gt; 11   25.2059 -0.5423   25.2059   20.1927  3.022e+01 2.372e+00    1.29116
+#&gt; 12   25.4145  0.9017   25.4145   20.0576  3.077e+01 2.223e+00    1.09707
+#&gt; 13    5.1971 -0.6231    5.1971    4.6665  5.728e+00 6.646e-01    0.49235
+#&gt; 14    5.2141  1.0511    5.2141    4.6477  5.781e+00 6.446e-01    0.46046
+#&gt; 15    0.6622 -0.5416    0.6622    0.5460  7.783e-01 6.213e-02    0.03513
+#&gt; 16    0.6560  0.9018    0.6560    0.5383  7.737e-01 5.738e-02    0.03163
+#&gt;    EDx10 97.5%    EDx20 EDx20 2.5% EDx20 97.5%
+#&gt; 1    2.211e+03 2850.328  2.019e+03   3681.2703
+#&gt; 2    2.196e+03 2958.988  2.092e+03   3826.1457
+#&gt; 3    6.149e+02  981.743  8.254e+02   1138.0862
+#&gt; 4    6.014e+02 1010.061  8.414e+02   1178.7611
+#&gt; 5    3.070e+02  472.838  4.257e+02    520.0197
+#&gt; 6    2.905e+02  472.906  4.239e+02    521.8955
+#&gt; 7    4.337e+02  588.259  4.999e+02    676.6627
+#&gt; 8    4.181e+02  590.824  4.972e+02    684.4677
+#&gt; 9    5.431e+01   78.383  5.955e+01     97.2142
+#&gt; 10   5.396e+01   80.763  5.975e+01    101.7713
+#&gt; 11   3.454e+00    5.339  3.544e+00      7.1350
+#&gt; 12   3.348e+00    5.463  3.489e+00      7.4370
+#&gt; 13   8.369e-01    1.346  1.084e+00      1.6086
+#&gt; 14   8.288e-01    1.394  1.106e+00      1.6832
+#&gt; 15   8.912e-02    0.140  9.501e-02      0.1850
+#&gt; 16   8.314e-02    0.141  9.588e-02      0.1862</div></pre>
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+    <h2>Contents</h2>
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+      <li><a href="#format">Format</a></li>
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+    <h1>Dose-Response data for two substances X and Y</h1>
+    </div>
+
+    
+    <p>This is just a sample Lemna growth rate data set for two substances
+  arbitrarily named X and Y.</p>
+    
+
+    <pre><span class='fu'>data</span>(<span class='no'>XY</span>)</pre>
+        
+    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+    <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'>  <span class='co'>## Not run: demo(XY)</span></div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <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>
+
+  </div>
+</div>
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+      </footer>
+   </div>
+
+  </body>
+</html>
diff --git a/docs/reference/antifoul.html b/docs/reference/antifoul.html
index f5bc9fd..92fd8e8 100644
--- a/docs/reference/antifoul.html
+++ b/docs/reference/antifoul.html
@@ -72,9 +72,9 @@
     </div>
 
     
-    <p>This data set shows the response of the rat leukaemic cell line IPC-81 to 
+    <p>This data set shows the response of the rat leukaemic cell line IPC-81 to
   dilution series of tributyltin chloride (TBT) and Zink Pyrithione as retrieved
-  from the "cytotox" database of the UFT Department of Bioorganic Chemistry on 
+  from the "cytotox" database of the UFT Department of Bioorganic Chemistry on
   February 25, 2004</p>
     
 
diff --git a/docs/reference/checkcontrols.html b/docs/reference/checkcontrols.html
index 2b2eb8b..0e89c93 100644
--- a/docs/reference/checkcontrols.html
+++ b/docs/reference/checkcontrols.html
@@ -76,7 +76,9 @@
   experiments from a specified database.</p>
     
 
-    <pre><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>, <span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"Vibrio fischeri"</span>,
+    <pre><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>,
+                <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>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
@@ -99,9 +101,18 @@
     supported, as well as the database of ecotoxicity experiments "ecotox".</p></td>
     </tr>
     <tr>
+      <th>celltype</th>
+      <td><p>Only important if database "cytotox" is used.  Data for
+    "IPC-81", "C6", "NB4", "HeLa", "Jurkat" and "U937" are available.</p></td>
+    </tr>
+    <tr>
+      <th>enzymetype</th>
+      <td><p>Only important if database "enzymes" is used.
+    Data for "AChE", "GR" and "GST" are available.</p></td>
+    </tr>
+    <tr>
       <th>organism</th>
-      <td><p>The organism that was exposed to the chemical. Only important if the database
-    "ecotox" is used. Defaults to "Vibrio fischeri".</p></td>
+      <td><p>Only important if database "ecotox" is used.</p></td>
     </tr>
     <tr>
       <th>endpoint</th>
@@ -110,8 +121,8 @@
     </tr>
     <tr>
       <th>qcc</th>
-      <td><p>The type of quality control charts to be plotted. By default, an R chart 
-    (showing ranges of control values within plates/experiments), and an 
+      <td><p>The type of quality control charts to be plotted. By default, an R chart
+    (showing ranges of control values within plates/experiments), and an
     xbar chart (showing means) are generated.</p></td>
     </tr>
     </table>
@@ -136,8 +147,8 @@
 
     <h2>Author</h2>
     
-  Johannes Ranke 
-  <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> 
+  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>
diff --git a/docs/reference/checkexperiment.html b/docs/reference/checkexperiment.html
index e22705d..277bfd5 100644
--- a/docs/reference/checkexperiment.html
+++ b/docs/reference/checkexperiment.html
@@ -120,8 +120,8 @@
 
     <h2>Author</h2>
     
-  Johannes Ranke 
-  <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> 
+  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>
diff --git a/docs/reference/checksubstance.html b/docs/reference/checksubstance.html
index 0fbca62..60ae6e3 100644
--- a/docs/reference/checksubstance.html
+++ b/docs/reference/checksubstance.html
@@ -122,12 +122,12 @@
     </tr>
     <tr>
       <th>whereClause</th>
-      <td><p>With this argument, additional conditions for the SQL query can be set, 
+      <td><p>With this argument, additional conditions for the SQL query can be set,
     e.g. "plate != 710". The default is 1 (in SQL syntax this means TRUE).</p></td>
     </tr>
     <tr>
       <th>ok</th>
-      <td><p>With the default value "%", all data in the database is retrieved for the 
+      <td><p>With the default value "%", all data in the database is retrieved for the
     specified substance.</p></td>
     </tr>
     </table>
@@ -153,8 +153,8 @@
 
     <h2>Author</h2>
     
-  Johannes Ranke 
-  <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> 
+  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>
diff --git a/docs/reference/drcfit.html b/docs/reference/drcfit.html
index 75a168a..e7de303 100644
--- a/docs/reference/drcfit.html
+++ b/docs/reference/drcfit.html
@@ -165,10 +165,10 @@
   <dt>mtype</dt><dd><p>If the data did not show a mean response &lt; 0.5 at the highest dose level,
     the modeltype is set to &#8220;inactive&#8221;. If the mean response at the
     lowest dose is smaller than 0.5, the modeltype is set to &#8220;active&#8221;.
-    In both cases, no fitting procedure is carried out. If the fitted ED50 
+    In both cases, no fitting procedure is carried out. If the fitted ED50
     is higher than the highest dose, &#8220;no fit&#8221; is given here.</p></dd>
   <dt>logED50</dt><dd><p>The decadic logarithm of the ED50</p></dd>
-  <dt>low %</dt><dd><p>The lower bound of the confidence interval of log ED50. 
+  <dt>low %</dt><dd><p>The lower bound of the confidence interval of log ED50.
     The name of the column depends on the requested confidence <code>level</code>.</p></dd>
   <dt>high %</dt><dd><p>The higher bound of the confidence interval of log ED50.
     The name of the column depends on the requested confidence <code>level</code>.</p></dd>
@@ -176,11 +176,11 @@
   <dt>sigma</dt><dd><p>The square root of the estimated variance of the random error as returned
     by <code>summary.drc</code>.</p></dd>
   <dt>a</dt><dd><p>For the linlogit model, this is the parameter e from <code>BC.4</code>.
-    For the probit and the logit model, this is the ED50. For the weibull 
-    model, this is parameter e from <code>W1.2</code>. Note that the Weibull 
+    For the probit and the logit model, this is the ED50. For the weibull
+    model, this is parameter e from <code>W1.2</code>. Note that the Weibull
     model is fitted to the untransformed data.</p></dd>
   <dt>b</dt><dd><p>For the linlogit, probit, logit and weibull models, these are the
-    parameters b from <code>BC.4</code>, <code>LN.2</code>, 
+    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>
@@ -236,7 +236,7 @@
 
     <h2>Author</h2>
     
-  Johannes Ranke <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> 
+  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 e369c5c..dd5be7b 100644
--- a/docs/reference/drdata.html
+++ b/docs/reference/drdata.html
@@ -95,7 +95,7 @@
     <tr>
       <th>db</th>
       <td><p>The database to be used. Currently, the databases "cytotox", "enzymes"
-    and "ecotox" of the UFT Department of Bioorganic Chemistry are 
+    and "ecotox" of the UFT Department of Bioorganic Chemistry are
     supported (default is "cytotox").</p></td>
     </tr>
     <tr>
@@ -119,7 +119,7 @@
     </tr>
     <tr>
       <th>whereClause</th>
-      <td><p>With this argument, additional conditions for the SQL query can be set, 
+      <td><p>With this argument, additional conditions for the SQL query can be set,
     e.g. "plate != 710" (i.e. "Do not retrieve data for plate 710"). The
     default is 1 (in SQL syntax this means TRUE).</p></td>
     </tr>
@@ -222,8 +222,8 @@
 
     <h2>Author</h2>
     
-  Johannes Ranke 
-  <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> 
+  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>
diff --git a/docs/reference/drfit.html b/docs/reference/drfit.html
index 7acce23..2de949f 100644
--- a/docs/reference/drfit.html
+++ b/docs/reference/drfit.html
@@ -196,9 +196,8 @@
   parameter <code>a</code> that is reported coincides with the logED50, i.e the
   logED50 is one of the model parameters that is being fitted. Therefore,
   a confidence interval for the confidence level <code>level</code> is calculated
-  using the <code>confint.nls</code> function and listed.
-  
-  The following variables are in the dataframe:</p>
+  using the <code>confint.nls</code> function and listed.</p>
+<p>The following variables are in the dataframe:</p>
 <dt>Substance</dt><dd><p>The name of the substance</p></dd>
   <dt>ndl</dt><dd><p>The number of dose levels in the raw data</p></dd>
   <dt>n</dt><dd><p>The total number of data points in the raw data used for the fit</p></dd>
@@ -207,10 +206,10 @@
   <dt>mtype</dt><dd><p>If the data did not show a mean response &lt; 0.5 at the highest dose level,
     the modeltype is set to &#8220;inactive&#8221;. If the mean response at the
     lowest dose is smaller than 0.5, the modeltype is set to &#8220;active&#8221;.
-    In both cases, no fitting procedure is carried out. If the fitted ED50 
+    In both cases, no fitting procedure is carried out. If the fitted ED50
     is higher than the highest dose, &#8220;no fit&#8221; is given here.</p></dd>
   <dt>logED50</dt><dd><p>The decadic logarithm of the ED50</p></dd>
-  <dt>low %</dt><dd><p>The lower bound of the confidence interval of log ED50. 
+  <dt>low %</dt><dd><p>The lower bound of the confidence interval of log ED50.
     The name of the column depends on the requested confidence <code>level</code>.</p></dd>
   <dt>high %</dt><dd><p>The higher bound of the confidence interval of log ED50.
     The name of the column depends on the requested confidence <code>level</code>.</p></dd>
@@ -277,8 +276,8 @@
 
     <h2>Author</h2>
     
-  Johannes Ranke 
-  <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> 
+  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>
diff --git a/docs/reference/drplot.html b/docs/reference/drplot.html
index eff1338..9a678e1 100644
--- a/docs/reference/drplot.html
+++ b/docs/reference/drplot.html
@@ -72,7 +72,7 @@
     </div>
 
     
-    <p>Produce graphics of dose-response data and dose-response relationships 
+    <p>Produce graphics of dose-response data and dose-response relationships
   either combined or separately, for one or more substances.</p>
     
 
@@ -110,7 +110,7 @@
     </tr>
     <tr>
       <th>ctype</th>
-      <td><p>This argument decides if horizontal lines are drawn to show the scatter of 
+      <td><p>This argument decides if horizontal lines are drawn to show the scatter of
     the control values (dose = 0), if there are more than three of them.
     Defaults to "none", further allowed values are "std" and "conf" for
     displaying the standard deviation of the controls or the confidence
@@ -159,13 +159,13 @@
     </tr>
     <tr>
       <th>postscript</th>
-      <td><p>If TRUE, (a) postscript graph(s) will be created. Otherwise, and if 
+      <td><p>If TRUE, (a) postscript graph(s) will be created. Otherwise, and if
     the pdf and png arguments are also FALSE, graphics will be
     displayed with a screen graphics device.</p></td>
     </tr>
     <tr>
       <th>pdf</th>
-      <td><p>If TRUE, (a) pdf graph(s) will be created. Otherwise, and if 
+      <td><p>If TRUE, (a) pdf graph(s) will be created. Otherwise, and if
     the postscript, and png arguments are also FALSE, graphics will be
     displayed with a screen graphics device.</p></td>
     </tr>
@@ -177,7 +177,7 @@
     </tr>
     <tr>
       <th>bw</th>
-      <td><p>A boolean deciding if the plots will be black and white or not. Default 
+      <td><p>A boolean deciding if the plots will be black and white or not. Default
     is TRUE.</p></td>
     </tr>
     <tr>
@@ -245,8 +245,8 @@
 
     <h2>Author</h2>
     
-  Johannes Ranke 
-  <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> 
+  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>
diff --git a/docs/reference/linlogitf.html b/docs/reference/linlogitf.html
new file mode 100644
index 0000000..8b9ba0d
--- /dev/null
+++ b/docs/reference/linlogitf.html
@@ -0,0 +1,149 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Linear-logistic function — linlogitf • drfit</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+  </head>
+
+  <body>
+    <div class="container template-reference-topic">
+      <header>
+      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <a class="navbar-brand" href="../index.html">drfit</a>
+    </div>
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+      </ul>
+      
+      <ul class="nav navbar-nav navbar-right">
+        
+      </ul>
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+      </header>
+
+      <div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Linear-logistic function</h1>
+    </div>
+
+    
+    <p>Helper function describing a special type of dose-response curves, showing a stimulus
+  at subtoxic doses.</p>
+    
+
+    <pre><span class='fu'>linlogitf</span>(<span class='no'>x</span>,<span class='no'>k</span>,<span class='no'>f</span>,<span class='no'>mu</span>,<span class='no'>b</span>)</pre>
+    
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>x</th>
+      <td><p>In this context, the x variable is the dose.</p></td>
+    </tr>
+    <tr>
+      <th>k</th>
+      <td><p>In the drfit functions, k is set to 1.</p></td>
+    </tr>
+    <tr>
+      <th>f</th>
+      <td><p>One of the parameters describing the curve shape.</p></td>
+    </tr>
+    <tr>
+      <th>mu</th>
+      <td><p>The parameter describing the location of the curve (log ED50).</p></td>
+    </tr>
+    <tr>
+      <th>b</th>
+      <td><p>One of the parameters describing the curve shape.</p></td>
+    </tr>
+    </table>
+    
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>The response at dose x.</p>
+    
+    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+    <p>van Ewijk, P. H. and Hoekstra, J. A. (1993) <em>Ecotox Environ Safety</em>
+  <b>25</b> 25-32</p>
+    
+
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      <li><a href="#arguments">Arguments</a></li>
+      
+      <li><a href="#value">Value</a></li>
+
+      <li><a href="#references">References</a></li>
+          </ul>
+
+    <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>
+
+  </div>
+</div>
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+      </footer>
+   </div>
+
+  </body>
+</html>
diff --git a/docs/reference/pyrithione.html b/docs/reference/pyrithione.html
new file mode 100644
index 0000000..7496be2
--- /dev/null
+++ b/docs/reference/pyrithione.html
@@ -0,0 +1,125 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Cytotoxicity data for different pyrithionates and related species — pyrithione • drfit</title>
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+  <a href="../reference/index.html">Reference</a>
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+    <h1>Cytotoxicity data for different pyrithionates and related species</h1>
+    </div>
+
+    
+    <p>This data shows the cytotoxicity of pyrithione salts as well as the free
+ pyrithione, its oxidation product and some other related compounds to the
+ IPC-81 cell line.</p>
+    
+
+    <pre><span class='fu'>data</span>(<span class='no'>pyrithione</span>)</pre>
+        
+    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+    <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>
+
+    <p>Doose C, Ranke J, Stock F, Bottin-Weber U, Jastorff B (2004)
+  Structure-activity relationships of pyrithiones - IPC-81 toxicity tests with
+  antifouling biocide zinc pyrithione and structural analogues. Green Chemistry
+  6(5) 259-266</p>
+    
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'>  <span class='co'>## Not run: demo(pyrithione)</span></div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <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>
+
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