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| -rw-r--r-- | R/checkcontrols.R | 65 | ||||
| -rw-r--r-- | check.log | 5 | ||||
| -rw-r--r-- | docs/index.html | 2 | ||||
| -rw-r--r-- | docs/reference/IM1xIPC81.html | 196 | ||||
| -rw-r--r-- | docs/reference/IM1xVibrio.html | 233 | ||||
| -rw-r--r-- | docs/reference/XY.html | 121 | ||||
| -rw-r--r-- | docs/reference/antifoul.html | 4 | ||||
| -rw-r--r-- | docs/reference/checkcontrols.html | 25 | ||||
| -rw-r--r-- | docs/reference/checkexperiment.html | 4 | ||||
| -rw-r--r-- | docs/reference/checksubstance.html | 8 | ||||
| -rw-r--r-- | docs/reference/drcfit.html | 12 | ||||
| -rw-r--r-- | docs/reference/drdata.html | 8 | ||||
| -rw-r--r-- | docs/reference/drfit.html | 13 | ||||
| -rw-r--r-- | docs/reference/drplot.html | 14 | ||||
| -rw-r--r-- | docs/reference/linlogitf.html | 149 | ||||
| -rw-r--r-- | docs/reference/pyrithione.html | 125 |
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", @@ -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> + <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>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells — IM1xIPC81 • 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>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'><-</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> +#> <span class='message'>IM16 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>IM17 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'>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'><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> +#> <span class='message'>IM16 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>IM17 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>IM18 BF4: Fitting data...</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'></span> +#> <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'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma +#> 1 IM13 BF4 9 81 0.5918 3.000 inactive NA NA NA microM NA +#> 2 IM14 BF4 20 216 -0.0103 3.176 no fit NA NA NA microM NA +#> 3 IM15 BF4 9 135 0.5918 3.000 inactive NA NA NA microM NA +#> 4 IM16 BF4 9 108 0.5918 3.000 inactive NA NA NA microM NA +#> 5 IM17 BF4 9 81 0.5918 3.000 linlogit 2.5786 2.506 2.6617 microM 0.2376 +#> 6 IM18 BF4 9 135 0.5918 3.000 linlogit 1.6806 1.623 1.7419 microM 0.2325 +#> 7 IM19 BF4 9 81 0.5918 3.000 linlogit 1.6496 1.598 1.7031 microM 0.1453 +#> 8 IM1-10 BF4 11 162 -0.0103 3.000 linlogit 0.7697 0.687 0.8544 microM 0.2988 +#> a b c ED50 ED50 2.5% ED50 97.5% EDx10 +#> 1 NA NA NA NA NA NA NA +#> 2 NA NA NA NA NA NA NA +#> 3 NA NA NA NA NA NA NA +#> 4 NA NA NA NA NA NA NA +#> 5 2.5786 2.300 0.01468 378.941 320.424 458.918 230.782 +#> 6 1.6806 2.237 0.05719 47.930 41.973 55.194 27.367 +#> 7 1.6496 1.977 0.10956 44.628 39.671 50.483 23.031 +#> 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'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma +#> 1 IM13 BF4 9 81 0.5918 3.000 inactive NA NA NA microM NA +#> 2 IM14 BF4 20 216 -0.0103 3.176 linlogit NA NA NA microM 0.1529 +#> 3 IM15 BF4 9 135 0.5918 3.000 inactive NA NA NA microM NA +#> 4 IM16 BF4 9 108 0.5918 3.000 inactive NA NA NA microM NA +#> 5 IM17 BF4 9 81 0.5918 3.000 linlogit 2.5786 2.4935 2.6497 microM 0.2376 +#> 6 IM18 BF4 9 135 0.5918 3.000 linlogit 1.6806 1.6168 1.7362 microM 0.2325 +#> 7 IM19 BF4 9 81 0.5918 3.000 linlogit 1.6496 1.5940 1.6990 microM 0.1453 +#> 8 IM1-10 BF4 11 162 -0.0103 3.000 linlogit 0.7697 0.6774 0.8458 microM 0.2988 +#> a b c ED50 ED50 2.5% ED50 97.5% EDx10 EDx10 2.5% +#> 1 NA NA NA NA NA NA NA NA +#> 2 5.390e+15 0.3148 -0.0001736 NA NA NA NA NA +#> 3 NA NA NA NA NA NA NA NA +#> 4 NA NA NA NA NA NA NA NA +#> 5 1.281e+02 2.3001 0.0146821 378.964 311.555 446.372 230.790 202.915 +#> 6 2.079e+01 2.2373 0.0571925 47.930 41.382 54.478 27.367 23.809 +#> 7 1.342e+01 1.9773 0.1094542 44.630 39.260 50.000 23.036 20.614 +#> 8 2.258e+00 1.9362 0.4580784 5.884 4.758 7.011 2.835 2.181 +#> EDx10 97.5% +#> 1 NA +#> 2 NA +#> 3 NA +#> 4 NA +#> 5 258.665 +#> 6 30.925 +#> 7 25.459 +#> 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> + + <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/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 @@ +<!-- 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>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri — IM1xVibrio • 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>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'><-</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> +#> <span class='message'>IM15 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'>IM16 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'>IM17 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'>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='message'>Waiting for profiling to be done...</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='message'>Waiting for profiling to be done...</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='output co'>#> <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'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma +#> 1 IM13 BF4 13 22 -5.301 4.699 probit 3.9399 3.8636 4.0160 microM 0.06303 +#> 2 IM13 BF4 13 22 -5.301 4.699 logit 3.9461 3.8708 4.0211 microM 0.06188 +#> 3 IM14 BF4 12 57 -4.301 4.699 probit 3.5442 3.5030 3.5855 microM 0.05905 +#> 4 IM14 BF4 12 57 -4.301 4.699 logit 3.5465 3.5044 3.5885 microM 0.06030 +#> 5 IM15 BF4 7 20 -0.301 4.699 probit 3.1398 3.1136 3.1662 microM 0.02695 +#> 6 IM15 BF4 7 20 -0.301 4.699 logit 3.1387 3.1118 3.1659 microM 0.02723 +#> 7 IM16 BF4 13 30 -4.301 4.699 probit 3.1804 3.1436 3.2176 microM 0.04514 +#> 8 IM16 BF4 13 30 -4.301 4.699 logit 3.1814 3.1440 3.2190 microM 0.04553 +#> 9 IM17 BF4 10 20 -1.301 4.699 probit 2.4317 2.3681 2.4951 microM 0.04773 +#> 10 IM17 BF4 10 20 -1.301 4.699 logit 2.4353 2.3672 2.5026 microM 0.05050 +#> 11 IM18 BF4 10 17 -2.301 2.699 probit 1.4015 1.3147 1.4881 microM 0.05611 +#> 12 IM18 BF4 10 17 -2.301 2.699 logit 1.4051 1.3129 1.4966 microM 0.05898 +#> 13 IM19 BF4 13 22 -5.301 2.699 probit 0.7158 0.6704 0.7592 microM 0.02956 +#> 14 IM19 BF4 13 22 -5.301 2.699 logit 0.7172 0.6689 0.7635 microM 0.03210 +#> 15 IM1-10 BF4 11 20 -6.301 2.699 probit -0.1790 -0.2569 -0.1037 microM 0.04099 +#> 16 IM1-10 BF4 11 20 -6.301 2.699 logit -0.1831 -0.2620 -0.1055 microM 0.04192 +#> a b ED50 ED50 2.5% ED50 97.5% EDx10 EDx20 +#> 1 3.9399 0.5763 8707.8956 7305.0279 1.038e+04 1.590e+03 2850.222 +#> 2 3.9461 0.3426 8832.9407 7426.2282 1.050e+04 1.561e+03 2959.147 +#> 3 3.5442 0.6561 3501.1558 3184.3196 3.851e+03 5.051e+02 981.759 +#> 4 3.5465 0.3911 3519.5779 3194.6808 3.877e+03 4.867e+02 1010.014 +#> 5 3.1398 0.5527 1379.9037 1298.9533 1.466e+03 2.701e+02 472.823 +#> 6 3.1387 0.3347 1376.4086 1293.7152 1.465e+03 2.532e+02 472.911 +#> 7 3.1804 0.4882 1515.0421 1391.8150 1.650e+03 3.588e+02 588.292 +#> 8 3.1814 0.2957 1518.4650 1393.2665 1.656e+03 3.401e+02 590.840 +#> 9 2.4317 0.6387 270.2279 233.3814 3.127e+02 4.105e+01 78.382 +#> 10 2.4353 0.3810 272.4409 232.9287 3.182e+02 3.965e+01 80.754 +#> 11 1.4015 0.8009 25.2069 20.6383 3.077e+01 2.372e+00 5.340 +#> 12 1.4051 0.4816 25.4135 20.5545 3.138e+01 2.222e+00 5.463 +#> 13 0.7158 0.6969 5.1975 4.6814 5.744e+00 6.647e-01 1.347 +#> 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'><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> +#> <span class='message'>IM15 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>IM16 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>IM17 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>IM18 BF4: Fitting data...</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'></span> +#> <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'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma +#> 1 IM13 BF4 13 22 -5.301 4.699 probit 3.9399 3.8563 4.0100 microM 0.06303 +#> 2 IM13 BF4 13 22 -5.301 4.699 logit 3.9461 3.8637 4.0153 microM 0.06188 +#> 3 IM14 BF4 12 57 -4.301 4.699 probit 3.5442 3.5009 3.5836 microM 0.05905 +#> 4 IM14 BF4 12 57 -4.301 4.699 logit 3.5465 3.5023 3.5866 microM 0.06030 +#> 5 IM15 BF4 7 20 -0.301 4.699 probit 3.1398 3.1127 3.1654 microM 0.02695 +#> 6 IM15 BF4 7 20 -0.301 4.699 logit 3.1387 3.1109 3.1649 microM 0.02723 +#> 7 IM16 BF4 13 30 -4.301 4.699 probit 3.1804 3.1419 3.2158 microM 0.04514 +#> 8 IM16 BF4 13 30 -4.301 4.699 logit 3.1814 3.1424 3.2172 microM 0.04553 +#> 9 IM17 BF4 10 20 -1.301 4.699 probit 2.4317 2.3632 2.4909 microM 0.04773 +#> 10 IM17 BF4 10 20 -1.301 4.699 logit 2.4353 2.3618 2.4981 microM 0.05050 +#> 11 IM18 BF4 10 17 -2.301 2.699 probit 1.4015 1.3052 1.4803 microM 0.05611 +#> 12 IM18 BF4 10 17 -2.301 2.699 logit 1.4051 1.3023 1.4881 microM 0.05898 +#> 13 IM19 BF4 13 22 -5.301 2.699 probit 0.7158 0.6690 0.7580 microM 0.02956 +#> 14 IM19 BF4 13 22 -5.301 2.699 logit 0.7172 0.6672 0.7620 microM 0.03210 +#> 15 IM1-10 BF4 11 20 -6.301 2.699 probit -0.1790 -0.2628 -0.1088 microM 0.04099 +#> 16 IM1-10 BF4 11 20 -6.301 2.699 logit -0.1831 -0.2690 -0.1114 microM 0.04192 +#> a b ED50 ED50 2.5% ED50 97.5% EDx10 EDx10 2.5% +#> 1 8707.5571 -0.7536 8707.5571 7183.0127 1.023e+04 1.590e+03 968.72501 +#> 2 8832.8773 1.2676 8832.8773 7306.8669 1.036e+04 1.561e+03 925.39582 +#> 3 3501.1967 -0.6619 3501.1967 3168.9639 3.833e+03 5.051e+02 395.26341 +#> 4 3519.5773 1.1105 3519.5773 3179.2923 3.860e+03 4.866e+02 371.84710 +#> 5 1379.9019 -0.7858 1379.9019 1296.3162 1.463e+03 2.701e+02 233.25320 +#> 6 1376.4086 1.2976 1376.4086 1290.8397 1.462e+03 2.531e+02 215.79719 +#> 7 1515.0427 -0.8896 1515.0427 1386.3308 1.644e+03 3.588e+02 283.79434 +#> 8 1518.4644 1.4686 1518.4644 1387.9173 1.649e+03 3.401e+02 262.20564 +#> 9 270.2279 -0.6800 270.2279 230.7905 3.097e+02 4.105e+01 27.78507 +#> 10 272.4526 1.1401 272.4526 230.0588 3.148e+02 3.966e+01 25.34948 +#> 11 25.2059 -0.5423 25.2059 20.1927 3.022e+01 2.372e+00 1.29116 +#> 12 25.4145 0.9017 25.4145 20.0576 3.077e+01 2.223e+00 1.09707 +#> 13 5.1971 -0.6231 5.1971 4.6665 5.728e+00 6.646e-01 0.49235 +#> 14 5.2141 1.0511 5.2141 4.6477 5.781e+00 6.446e-01 0.46046 +#> 15 0.6622 -0.5416 0.6622 0.5460 7.783e-01 6.213e-02 0.03513 +#> 16 0.6560 0.9018 0.6560 0.5383 7.737e-01 5.738e-02 0.03163 +#> EDx10 97.5% EDx20 EDx20 2.5% EDx20 97.5% +#> 1 2.211e+03 2850.328 2.019e+03 3681.2703 +#> 2 2.196e+03 2958.988 2.092e+03 3826.1457 +#> 3 6.149e+02 981.743 8.254e+02 1138.0862 +#> 4 6.014e+02 1010.061 8.414e+02 1178.7611 +#> 5 3.070e+02 472.838 4.257e+02 520.0197 +#> 6 2.905e+02 472.906 4.239e+02 521.8955 +#> 7 4.337e+02 588.259 4.999e+02 676.6627 +#> 8 4.181e+02 590.824 4.972e+02 684.4677 +#> 9 5.431e+01 78.383 5.955e+01 97.2142 +#> 10 5.396e+01 80.763 5.975e+01 101.7713 +#> 11 3.454e+00 5.339 3.544e+00 7.1350 +#> 12 3.348e+00 5.463 3.489e+00 7.4370 +#> 13 8.369e-01 1.346 1.084e+00 1.6086 +#> 14 8.288e-01 1.394 1.106e+00 1.6832 +#> 15 8.912e-02 0.140 9.501e-02 0.1850 +#> 16 8.314e-02 0.141 9.588e-02 0.1862</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/XY.html b/docs/reference/XY.html new file mode 100644 index 0000000..a585270 --- /dev/null +++ b/docs/reference/XY.html @@ -0,0 +1,121 @@ +<!-- 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>Dose-Response data for two substances X and Y — XY • drfit</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" 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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>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 < 0.5 at the highest dose level, the modeltype is set to “inactive”. If the mean response at the lowest dose is smaller than 0.5, the modeltype is set to “active”. - 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, “no fit” 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 < 0.5 at the highest dose level, the modeltype is set to “inactive”. If the mean response at the lowest dose is smaller than 0.5, the modeltype is set to “active”. - 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, “no fit” 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> + +<!-- 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>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> + + </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> |