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| -rw-r--r-- | GNUmakefile | 16 | ||||
| -rw-r--r-- | docs/authors.html | 99 | ||||
| -rw-r--r-- | docs/index.html | 88 | ||||
| -rw-r--r-- | docs/jquery.sticky-kit.min.js | 9 | ||||
| -rw-r--r-- | docs/link.svg | 12 | ||||
| -rw-r--r-- | docs/pkgdown.css | 137 | ||||
| -rw-r--r-- | docs/pkgdown.js | 8 | ||||
| -rw-r--r-- | docs/reference/antifoul.html | 160 | ||||
| -rw-r--r-- | docs/reference/checkcontrols.html | 159 | ||||
| -rw-r--r-- | docs/reference/checkexperiment.html | 143 | ||||
| -rw-r--r-- | docs/reference/checksubstance.html | 176 | ||||
| -rw-r--r-- | docs/reference/drcfit.html | 251 | ||||
| -rw-r--r-- | docs/reference/drdata.html | 245 | ||||
| -rw-r--r-- | docs/reference/drfit-package-9.png | bin | 0 -> 20004 bytes | |||
| -rw-r--r-- | docs/reference/drfit-package.html | 141 | ||||
| -rw-r--r-- | docs/reference/drfit.html | 300 | ||||
| -rw-r--r-- | docs/reference/drplot.html | 268 | ||||
| -rw-r--r-- | docs/reference/index.html | 195 |
18 files changed, 2400 insertions, 7 deletions
diff --git a/GNUmakefile b/GNUmakefile index 64aa9d4..6b5e68c 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -1,7 +1,7 @@ PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION) PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION) PKGSRC := $(shell basename $(PWD)) -TGZ := ../$(PKGNAME)_$(PKGVERS).tar.gz +TGZ := $(PKGNAME)_$(PKGVERS).tar.gz # Specify the directory holding R binaries. 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Author, maintainer. + </p> + </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/index.html b/docs/index.html new file mode 100644 index 0000000..3ad6d4a --- /dev/null +++ b/docs/index.html @@ -0,0 +1,88 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> +<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 Evaluation • 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-home"> + <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="contents col-md-9"> + A somewhat outdated package of basic and easy-to-use functions for + fitting dose-response curves to continuous dose-response data, calculating some + (eco)toxicological parameters and plotting the results. Please consider using + the more powerful and actively developed 'drc' package. Functions that are + fitted are the cumulative density function of the lognormal distribution + (probit fit), of the logistic distribution (logit fit), of the weibull + distribution (weibull fit) and a linear-logistic model ("linlogit" fit), + derived from the latter, which is used to describe data showing stimulation at + low doses (hormesis). In addition, functions checking, plotting and retrieving + dose-response data retrieved from a database accessed via RODBC are included. + As an alternative to the original fitting methods, the algorithms from the drc + package can be used. + </div> + + <div class="col-md-3" id="sidebar"> + <h2>Links</h2> +<ul class="list-unstyled"> +<li>Download from CRAN at <br><a href="https://cran.r-project.org/package=drfit">https://cran.r-project.org/package=drfit</a> +</li> +</ul> +<h2>License</h2> +<p>GPL (>= 2)</p> +<h2>Developers</h2> +<ul class="list-unstyled"> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer </small> </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/jquery.sticky-kit.min.js b/docs/jquery.sticky-kit.min.js new file mode 100644 index 0000000..e2a3c6d --- /dev/null +++ b/docs/jquery.sticky-kit.min.js @@ -0,0 +1,9 @@ +/* + Sticky-kit v1.1.2 | WTFPL | Leaf Corcoran 2015 | http://leafo.net +*/ +(function(){var b,f;b=this.jQuery||window.jQuery;f=b(window);b.fn.stick_in_parent=function(d){var A,w,J,n,B,K,p,q,k,E,t;null==d&&(d={});t=d.sticky_class;B=d.inner_scrolling;E=d.recalc_every;k=d.parent;q=d.offset_top;p=d.spacer;w=d.bottoming;null==q&&(q=0);null==k&&(k=void 0);null==B&&(B=!0);null==t&&(t="is_stuck");A=b(document);null==w&&(w=!0);J=function(a,d,n,C,F,u,r,G){var v,H,m,D,I,c,g,x,y,z,h,l;if(!a.data("sticky_kit")){a.data("sticky_kit",!0);I=A.height();g=a.parent();null!=k&&(g=g.closest(k)); +if(!g.length)throw"failed to find stick parent";v=m=!1;(h=null!=p?p&&a.closest(p):b("<div />"))&&h.css("position",a.css("position"));x=function(){var c,f,e;if(!G&&(I=A.height(),c=parseInt(g.css("border-top-width"),10),f=parseInt(g.css("padding-top"),10),d=parseInt(g.css("padding-bottom"),10),n=g.offset().top+c+f,C=g.height(),m&&(v=m=!1,null==p&&(a.insertAfter(h),h.detach()),a.css({position:"",top:"",width:"",bottom:""}).removeClass(t),e=!0),F=a.offset().top-(parseInt(a.css("margin-top"),10)||0)-q, +u=a.outerHeight(!0),r=a.css("float"),h&&h.css({width:a.outerWidth(!0),height:u,display:a.css("display"),"vertical-align":a.css("vertical-align"),"float":r}),e))return l()};x();if(u!==C)return D=void 0,c=q,z=E,l=function(){var b,l,e,k;if(!G&&(e=!1,null!=z&&(--z,0>=z&&(z=E,x(),e=!0)),e||A.height()===I||x(),e=f.scrollTop(),null!=D&&(l=e-D),D=e,m?(w&&(k=e+u+c>C+n,v&&!k&&(v=!1,a.css({position:"fixed",bottom:"",top:c}).trigger("sticky_kit:unbottom"))),e<F&&(m=!1,c=q,null==p&&("left"!==r&&"right"!==r||a.insertAfter(h), +h.detach()),b={position:"",width:"",top:""},a.css(b).removeClass(t).trigger("sticky_kit:unstick")),B&&(b=f.height(),u+q>b&&!v&&(c-=l,c=Math.max(b-u,c),c=Math.min(q,c),m&&a.css({top:c+"px"})))):e>F&&(m=!0,b={position:"fixed",top:c},b.width="border-box"===a.css("box-sizing")?a.outerWidth()+"px":a.width()+"px",a.css(b).addClass(t),null==p&&(a.after(h),"left"!==r&&"right"!==r||h.append(a)),a.trigger("sticky_kit:stick")),m&&w&&(null==k&&(k=e+u+c>C+n),!v&&k)))return v=!0,"static"===g.css("position")&&g.css({position:"relative"}), +a.css({position:"absolute",bottom:d,top:"auto"}).trigger("sticky_kit:bottom")},y=function(){x();return l()},H=function(){G=!0;f.off("touchmove",l);f.off("scroll",l);f.off("resize",y);b(document.body).off("sticky_kit:recalc",y);a.off("sticky_kit:detach",H);a.removeData("sticky_kit");a.css({position:"",bottom:"",top:"",width:""});g.position("position","");if(m)return null==p&&("left"!==r&&"right"!==r||a.insertAfter(h),h.remove()),a.removeClass(t)},f.on("touchmove",l),f.on("scroll",l),f.on("resize", +y),b(document.body).on("sticky_kit:recalc",y),a.on("sticky_kit:detach",H),setTimeout(l,0)}};n=0;for(K=this.length;n<K;n++)d=this[n],J(b(d));return this}}).call(this); diff --git a/docs/link.svg b/docs/link.svg new file mode 100644 index 0000000..88ad827 --- /dev/null +++ b/docs/link.svg @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="utf-8"?> +<!-- Generator: Adobe Illustrator 19.2.1, SVG Export Plug-In . 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+ display: block; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js new file mode 100644 index 0000000..c8b38c4 --- /dev/null +++ b/docs/pkgdown.js @@ -0,0 +1,8 @@ +$(function() { + $("#sidebar").stick_in_parent({offset_top: 40}); + $('body').scrollspy({ + target: '#sidebar', + offset: 60 + }); + +}); diff --git a/docs/reference/antifoul.html b/docs/reference/antifoul.html new file mode 100644 index 0000000..5a2b886 --- /dev/null +++ b/docs/reference/antifoul.html @@ -0,0 +1,160 @@ +<!-- 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 TBT and Zink Pyrithione in IPC-81 cells — antifoul • 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 TBT and Zink Pyrithione in IPC-81 cells</h1> + </div> + + + <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 + February 25, 2004</p> + + + <pre><span class='fu'>data</span>(<span class='no'>antifoul</span>)</pre> + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + + <p>A dataframe containing 135 and 81 data points for concentrations and responses + for TBT and Zink Pyrithione, respectively. Some additional columns from the + database are also present.</p> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + + <p><a href = 'http://www.uft.uni-bremen.de/chemie'>http://www.uft.uni-bremen.de/chemie</a></p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>rantifoul.ED50</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</span>, + <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>10</span>))</div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>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'>Zn Pyrithion: 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'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>rantifoul.ED50</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% +#> 1 TBT 38 135 -2.7093 2.3979 linlogit -0.15809 -0.26021 -0.050475 +#> 2 TBT 38 135 -2.7093 2.3979 probit -0.16436 -0.26504 -0.056498 +#> 3 TBT 38 135 -2.7093 2.3979 logit -0.16012 -0.26116 -0.052591 +#> 4 TBT 38 135 -2.7093 2.3979 weibull -0.11507 NA NA +#> 5 Zn Pyrithion 27 81 -2.1072 2.0000 linlogit -0.41329 -0.52932 -0.299799 +#> 6 Zn Pyrithion 27 81 -2.1072 2.0000 probit -0.39792 -0.50783 -0.291563 +#> 7 Zn Pyrithion 27 81 -2.1072 2.0000 logit -0.40035 -0.51049 -0.293501 +#> 8 Zn Pyrithion 27 81 -2.1072 2.0000 weibull -0.38795 NA NA +#> unit sigma a b c ED50 ED50 2.5% ED50 97.5% +#> 1 microM 0.19264 -0.15809 1.04065 -0.024165 0.69487 0.54927 0.89028 +#> 2 microM 0.19286 -0.16436 0.67637 NA 0.68493 0.54320 0.87801 +#> 3 microM 0.19199 -0.16012 0.41358 NA 0.69164 0.54808 0.88595 +#> 4 microM 0.18810 0.63743 1.28891 NA 0.76724 NA NA +#> 5 microM 0.22878 -0.41329 1.74249 0.610810 0.38611 0.29558 0.50142 +#> 6 microM 0.22866 -0.39792 0.41696 NA 0.40002 0.31058 0.51102 +#> 7 microM 0.22802 -0.40035 0.25395 NA 0.39779 0.30868 0.50874 +#> 8 microM 0.23008 0.47647 2.51561 NA 0.40931 NA NA +#> EDx10 +#> 1 0.085214 +#> 2 0.093077 +#> 3 0.085340 +#> 4 0.053392 +#> 5 0.120232 +#> 6 0.116872 +#> 7 0.110068 +#> 8 0.121166</div><div class='input'> +<span class='no'>rantifoul.drc</span> <span class='kw'><-</span> <span class='fu'><a href='drcfit.html'>drcfit</a></span>(<span class='no'>antifoul</span>, + <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>10</span>))</div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='error'>Error in ED50["1:50", "Lower"]: Indizierung außerhalb der Grenzen</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>rantifoul.drc</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='output co'>#> <span class='error'>Error in print(rantifoul.drc, digits = 5): Objekt 'rantifoul.drc' nicht gefunden</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/checkcontrols.html b/docs/reference/checkcontrols.html new file mode 100644 index 0000000..2b2eb8b --- /dev/null +++ b/docs/reference/checkcontrols.html @@ -0,0 +1,159 @@ +<!-- 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>Check raw data from range of plates or experiments — checkcontrols • drfit</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" 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+<!--[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>Check raw data from range of plates or experiments</h1> + </div> + + + <p>Report control data from a specified range of microtiter plates or + 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>, + <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> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>last</th> + <td><p>If <code>id</code> is not specified, this argument specifies the number of + plates/experiments that should be evaluated. The plates/experiments with + the hightest numbers are selected.</p></td> + </tr> + <tr> + <th>id</th> + <td><p>A numeric vector of integers, specifying the plates or experiments explicitly.</p></td> + </tr> + <tr> + <th>db</th> + <td><p>The database to be used. Currently, the microtiter plate databases + "cytotox", "enzymes" of the UFT Department of Bioorganic Chemistry are + supported, as well as the database of ecotoxicity experiments "ecotox".</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> + </tr> + <tr> + <th>endpoint</th> + <td><p>The endpoint that should be used for selecting the data. Only important if + the database "ecotox" is used. Defaults to "%".</p></td> + </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 + xbar chart (showing means) are generated.</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The function lists a report and shows two graphs.</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: checkcontrols(15)</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="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</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/checkexperiment.html b/docs/reference/checkexperiment.html new file mode 100644 index 0000000..e22705d --- /dev/null +++ b/docs/reference/checkexperiment.html @@ -0,0 +1,143 @@ +<!-- 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>Check raw data from a specified experiment or microtiter plate — checkexperiment • drfit</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> 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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>Check raw data from a specified experiment or microtiter plate</h1> + </div> + + + <p>Report metadata from a specified experiment or microtiter plate from a + specified database, box plot controls, and plot the dose-response data.</p> + + + <pre><span class='fu'>checkplate</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>) + <span class='fu'>checkexperiment</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"ecotox"</span>, <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>)</pre> + + <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>id</th> + <td><p>The id of the experiment or the plate identifying it within the database.</p></td> + </tr> + <tr> + <th>db</th> + <td><p>The database to be used. Currently, the microtiter plate databases + "cytotox", "enzymes" of the UFT Department of Bioorganic Chemistry are + supported, as well as the database of ecotoxicity experiments "ecotox".</p></td> + </tr> + <tr> + <th>endpoint</th> + <td><p>The endpoint that should be used for selecting the data. Only important if + the database "ecotox" is used. Defaults to "%".</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The function lists a report and shows two graphs.</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='co'># Check plate number 3 in the cytotox database</span> +<span class='co'>## Not run: checkplate(3)</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="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</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/checksubstance.html b/docs/reference/checksubstance.html new file mode 100644 index 0000000..0fbca62 --- /dev/null +++ b/docs/reference/checksubstance.html @@ -0,0 +1,176 @@ +<!-- 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>Check raw data for a specified substance — checksubstance • drfit</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link 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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>Check raw data for a specified substance</h1> + </div> + + + <p>Report metadata for a specified substance from a specified database, and plot + the data.</p> + + + <pre><span class='fu'>checksubstance</span>(<span class='no'>substance</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>, + <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>enzymetype</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"%"</span>, + <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>, + <span class='kw'>whereClause</span> <span class='kw'>=</span> <span class='st'>"1"</span>, <span class='kw'>ok</span> <span class='kw'>=</span> <span class='st'>"%"</span>)</pre> + + <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>substance</th> + <td><p>The name of the substance identifying it within the database.</p></td> + </tr> + <tr> + <th>db</th> + <td><p>The database to be used. Currently, the databases "cytotox" and "enzymes" + of the UFT Department of Bioorganic Chemistry are supported (default is + "cytotox").</p></td> + </tr> + <tr> + <th>experimentator</th> + <td><p>The name of the experimentator whose data is to be used. Default is "%", + which means that data from all experimentators are shown.</p></td> + </tr> + <tr> + <th>celltype</th> + <td><p>Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are + supported. Default is "%", i.e. data for any cell type will be + displayed.</p></td> + </tr> + <tr> + <th>enzymetype</th> + <td><p>Currently, only data for AChE, GR and GST are supported. The default value + is "%", i.e. data for any enzyme type will be displayed.</p></td> + </tr> + <tr> + <th>organism</th> + <td><p>The latin name of the tested organism, if the ecotox db was selected. The + default value is "%", i.e. data for any organism will be displayed.</p></td> + </tr> + <tr> + <th>endpoint</th> + <td><p>The endpoint that should be used for selecting the data. Only important if + the database "ecotox" is used. Defaults to "%".</p></td> + </tr> + <tr> + <th>whereClause</th> + <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 + specified substance.</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The function lists a report and shows one graph.</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='co'># Check substance IM14 BF4 in the cytotox database</span> +<span class='co'>## Not run: checksubstance("IM14 BF4")</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="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</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/drcfit.html b/docs/reference/drcfit.html new file mode 100644 index 0000000..ccf4641 --- /dev/null +++ b/docs/reference/drcfit.html @@ -0,0 +1,251 @@ +<!-- 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>Fit dose-response models using the drc package — drcfit • drfit</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" 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</div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Fit dose-response models using the drc package</h1> + </div> + + + <p>Fit dose-response relationships to dose-response data and calculate + biometric results for (eco)toxicity evaluation using the drc package</p> + + + <pre><span class='fu'>drcfit</span>(<span class='no'>data</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>probit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, + <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='kw'>NULL</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>data</th> + <td><p>A data frame containing dose-response data. The data frame has to contain + at least a factor called “substance”, a numeric vector “dose” + with the dose values, a vector called “unit” containing the unit + used for the dose and a numeric vector “response” with the response + values of the test system normalized between 0 and 1. Such a data frame can + be easily obtained if a compliant RODBC data source is available for use in + conjunction with the function <code><a href='drdata.html'>drdata</a></code>.</p> +<p>If there is a column called “ok” and it is set to “no fit” in + a specific line, then the corresponding data point will be excluded from + the fitting procedure, although it will be plotted.</p></td> + </tr> + <tr> + <th>probit</th> + <td><p>A boolean defining if cumulative density curves of normal distributions + are fitted against the decadic logarithm of the dose. Default ist TRUE. + Note that the parameter definitions used in the model are different to the + ones used in <code><a href='drfit.html'>drfit</a></code>. Parameter e from <code>LN.2</code> is listed + as a here, and parameter b from there is listed as b.</p></td> + </tr> + <tr> + <th>logit</th> + <td><p>A boolean defining if cumulative density curves of logistic distributions + <code>plogis</code> are fitted to the decadic logarithm of the dose. + Default is FALSE. + Again the parameter definitions used in the model are different to the + ones used in <code><a href='drfit.html'>drfit</a></code>. Parameter e from <code>LL.2</code> is listed + as a here, and parameter b from LL.2 is listed as b.</p></td> + </tr> + <tr> + <th>weibull</th> + <td><p>A boolean defining if Weibull dose-response models + (<code>W1.2</code> are fitted to the untransformed dose. Default is FALSE. + Note that the results differ from the ones obtained with + <code><a href='drfit.html'>drfit</a></code>, due to a different model specification.</p></td> + </tr> + <tr> + <th>linlogit</th> + <td><p>A boolean defining if the linear-logistic function + <code><a href='linlogitf.html'>linlogitf</a></code> as defined by van Ewijk and Hoekstra 1993 is + fitted to the data. Default is FALSE. Obtaining the ED50 (and EDx values + in general) uses <code>ED</code> internally and does not always give a + result.</p></td> + </tr> + <tr> + <th>level</th> + <td><p>The level for the confidence interval listed for the log ED50.</p></td> + </tr> + <tr> + <th>chooseone</th> + <td><p>If TRUE (default), the models are tried in the order linlogit, probit, + logit, weibull, and the first model that produces a valid fit is used. + If FALSE, all models that are set to TRUE and that can be fitted will be + reported.</p></td> + </tr> + <tr> + <th>EDx</th> + <td><p>A vector of inhibition values x in percent for which the corresponding doses + EDx should be reported.</p></td> + </tr> + <tr> + <th>showED50</th> + <td><p>If set to TRUE, the ED50 and its confidence interval on the original dose + scale (not log scale) is included in the output.</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>A dataframe with the attribute <code>models</code> holding a list of the fitted + dose-response models of class <code>nls</code>. The dataframe has at least + one line for each substance.</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> + <dt>lld</dt><dd><p>The decadic logarithm of the lowest dose</p></dd> + <dt>lhd</dt><dd><p>The total number of data points in the raw data used for the fit</p></dd> + <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 + 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. + 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> + <dt>unit</dt><dd><p>The unit used for the dose levels in the dose-response data</p></dd> + <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 + 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>, + <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> + <dt>c</dt><dd><p>Only the “linlogit” fit produces a third parameter <code>c</code>, which is + the parameter f from the <code>BC.4</code> function.</p></dd> + If the parameter showED50 was set to TRUE, the ED50 values and their + confidence intervals are also included on the original dose scale. + + If one or more response leves were specified in the argument EDx, + the corresponding dose levels are given in addition, together with their + confidence intervals as calculated by ED from the drc package. + + + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> + + <p>There is a demo for each dataset that can be accessed by + <code>demo(dataset)</code></p> + + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> + + <p>Further examples are given in help pages to the datasets + <code><a href='antifoul.html'>antifoul</a></code>, <code><a href='IM1xIPC81.html'>IM1xIPC81</a></code> and + <code><a href='IM1xVibrio.html'>IM1xVibrio</a></code>.</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>) +<span class='no'>r</span> <span class='kw'><-</span> <span class='fu'>drcfit</span>(<span class='no'>antifoul</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='error'>Error in ED50["1:50", "Lower"]: Indizierung außerhalb der Grenzen</span></div><div class='input'><span class='fu'>format</span>(<span class='no'>r</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='output co'>#> <span class='error'>Error in format(r, digits = 2): Objekt 'r' nicht gefunden</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="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#note">Note</a></li> + + <li><a href="#see-also">See also</a></li> + + <li><a href="#examples">Examples</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> + The functionality of the drc package used under the hood in this function + was written by Christian Ritz. + + </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/drdata.html b/docs/reference/drdata.html new file mode 100644 index 0000000..e369c5c --- /dev/null +++ b/docs/reference/drdata.html @@ -0,0 +1,245 @@ +<!-- 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>Get dose-response data via RODBC — drdata • 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>Get dose-response data via RODBC</h1> + </div> + + + <p>Get dose-response data from an adequate ODBC data source</p> + + + <pre><span class='fu'>drdata</span>(<span class='no'>substances</span>, <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"IPC-81"</span>, + <span class='kw'>enzymetype</span><span class='kw'>=</span><span class='st'>"AChE"</span>, <span class='kw'>organism</span><span class='kw'>=</span><span class='st'>"Vibrio fischeri"</span>, <span class='kw'>endpoint</span><span class='kw'>=</span><span class='st'>"Luminescence"</span>, + <span class='kw'>whereClause</span> <span class='kw'>=</span> <span class='st'>"1"</span>, <span class='kw'>ok</span> <span class='kw'>=</span> <span class='st'>"'ok','no fit'"</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>substances</th> + <td><p>A string or an array of strings with the substance names for + which dose-response data is to be retrieved.</p></td> + </tr> + <tr> + <th>experimentator</th> + <td><p>The name of the experimentator whose data is to be used. Default is "<!-- %", --> + which means that data from all experimentators are retrieved.</p></td> + </tr> + <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 + supported (default is "cytotox").</p></td> + </tr> + <tr> + <th>celltype</th> + <td><p>Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are + supported.</p></td> + </tr> + <tr> + <th>enzymetype</th> + <td><p>Currently, only data for AChE, GR and GST are supported.</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> + </tr> + <tr> + <th>endpoint</th> + <td><p>The endpoint that should be used for selecting the data. Only important if + the database "ecotox" is used. Defaults to "Luminescence".</p></td> + </tr> + <tr> + <th>whereClause</th> + <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> + <tr> + <th>ok</th> + <td><p>With the default value "'ok','no fit'", only data that has been checked and + set to "ok" or "no fit" in the database is retrieved. The argument "no fit" + will result in not using the data for fitting, but it will be plotted. + Another sensible argument would be "'ok','no fit','?'", in order to + additionally retrieve data which has not yet been checked.</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p></p> +<dt>data</dt><dd><p>A data frame with a factor describing the dose levels, the numeric dose + levels and a numeric column describing the response, as well as the entries + for plate, experimentator, performed (date of test performance), celltype, + unit (of the dose/concentration), and for the ok field in the database.</p></dd> + + + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + + <p>The function is currently only used for retrieving data from the + mysql database "cytotox" of the UFT Department of Bioorganic Chemistry. + Access to this database is limited to UFT staff. Additionally to the + installation of the RODBC package, it is required to set up a ODBC data + source with the name "cytotox", using an ODBC driver for mysql, probably + myODBC. Then, under Unix, you can use iodbc or unixodbc for setting up the + respective data source with data source name (DSN) "cytotox". For my + setting using unixodbc, I am using the file <code class="file">/etc/odbcinst.ini</code> + containing:</p><table><tr><td> + [MySQL] </td> +<td> </td> +</tr><tr><td> </td> +<td> + Description </td> +</tr><tr><td> = </td> +<td> MySQL driver for ODBC </td> +</tr><tr><td> + Driver </td> +<td> = </td> +</tr><tr><td> /usr/local/lib/libmyodbc.so </td> +<td> + Setup </td> +</tr><tr><td> = </td> +<td> /usr/lib/odbc/libodbcmyS.so </td> +</tr></table><p>and the file <code class="file">/etc/odbc.ini</code> containing:</p><table><tr><td> + [cytotox] </td> +<td> </td> +</tr><tr><td> </td> +<td> + Description </td> +</tr><tr><td> = </td> +<td> Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen </td> +</tr><tr><td> + Driver </td> +<td> = </td> +</tr><tr><td> MySQL </td> +<td> + Trace </td> +</tr><tr><td> = </td> +<td> Yes </td> +</tr><tr><td> + TraceFile </td> +<td> = </td> +</tr><tr><td> /tmp/odbc.log </td> +<td> + Database </td> +</tr><tr><td> = </td> +<td> cytotox </td> +</tr><tr><td> + Server </td> +<td> = </td> +</tr><tr><td> eckehaat </td> +<td> + Port </td> +</tr><tr><td> = </td> +<td> 3306 </td> +</tr></table> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='co'># Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81</span> +<span class='co'># cells</span> +<span class='co'>## Not run: drdata(c("TBT","ZnPT2"))</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="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#details">Details</a></li> + + <li><a href="#examples">Examples</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/drfit-package-9.png b/docs/reference/drfit-package-9.png Binary files differnew file mode 100644 index 0000000..1095620 --- /dev/null +++ b/docs/reference/drfit-package-9.png diff --git a/docs/reference/drfit-package.html b/docs/reference/drfit-package.html new file mode 100644 index 0000000..17611e7 --- /dev/null +++ b/docs/reference/drfit-package.html @@ -0,0 +1,141 @@ +<!-- 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"> + 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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 evaluation</h1> + </div> + + + <p>See <a href = '../DESCRIPTION'>../DESCRIPTION</a></p> + + + + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + + <p>There is an introductory article located in <a href = '../doc/drfit-Rnews.pdf'>../doc/drfit-Rnews.pdf</a>, +which will be published in the R News special edition on the use +of R for chemists.</p> + + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> + + <p>There is a demo for each dataset that can be accessed by + <code>demo(dataset)</code></p> + + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> + + <p>On CRAN, there is another, more statistically sophisticated package with +similar functionality called <code>drc</code>. I think the advantage of my package +is its user-friendliness.</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>) +<span class='no'>r</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</span>)</div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'>format</span>(<span class='no'>r</span>,<span class='kw'>digits</span><span class='kw'>=</span><span class='fl'>2</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma a +#> 1 TBT 38 135 -2.7 2.4 probit -0.16 -0.27 -0.056 microM 0.19 -0.16 +#> 2 Zn Pyrithion 27 81 -2.1 2.0 probit -0.40 -0.51 -0.292 microM 0.23 -0.40 +#> b +#> 1 0.68 +#> 2 0.42</div><div class='input'><span class='fu'><a href='drplot.html'>drplot</a></span>(<span class='no'>r</span>,<span class='no'>antifoul</span>,<span class='kw'>overlay</span><span class='kw'>=</span><span class='fl'>TRUE</span>,<span class='kw'>bw</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><img src='drfit-package-9.png' alt='' width='540' height='400' /></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="#details">Details</a></li> + + <li><a href="#note">Note</a></li> + + <li><a href="#see-also">See also</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + <h2>Author</h2> + +Author and Maintainer: Johannes Ranke <jranke@uni-bremen.de> + + </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/drfit.html b/docs/reference/drfit.html new file mode 100644 index 0000000..7acce23 --- /dev/null +++ b/docs/reference/drfit.html @@ -0,0 +1,300 @@ +<!-- 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>Fit dose-response models — drfit • drfit</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" 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+<!--[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>Fit dose-response models</h1> + </div> + + + <p>Fit dose-response relationships to dose-response data and calculate + biometric results for (eco)toxicity evaluation</p> + + + <pre><span class='fu'>drfit</span>(<span class='no'>data</span>, <span class='kw'>startlogED50</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>probit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, <span class='kw'>linlogitWrong</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>allWrong</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>ps0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>ls0</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>ws0</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>b0</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>f0</span> <span class='kw'>=</span> <span class='fl'>0</span>, + <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>EDx.tolerance</span> <span class='kw'>=</span> <span class='fl'>1e-4</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>data</th> + <td><p>A data frame containing dose-response data. The data frame has to contain + at least a factor called “substance”, a numeric vector “dose” + with the dose values, a vector called “unit” containing the unit + used for the dose and a numeric vector “response” with the response + values of the test system normalized between 0 and 1. Such a data frame can + be easily obtained if a compliant RODBC data source is available for use in + conjunction with the function <code><a href='drdata.html'>drdata</a></code>.</p> +<p>If there is a column called “ok” and it is set to “no fit” in + a specific line, then the corresponding data point will be excluded from + the fitting procedure, although it will be plotted.</p></td> + </tr> + <tr> + <th>startlogED50</th> + <td><p>Especially for the linlogit model, a suitable log10 of the ED50 has to be + given by the user, since it is not correctly estimated for data showing + hormesis with the default estimation method.</p></td> + </tr> + <tr> + <th>probit</th> + <td><p>A boolean defining if cumulative density curves of normal distributions + <code>pnorm</code> are fitted against the decadic logarithm of the dose. + Default ist TRUE.</p></td> + </tr> + <tr> + <th>logit</th> + <td><p>A boolean defining if cumulative density curves of logistic distributions + <code>plogis</code> are fitted to the decadic logarithm of the dose. + Default is FALSE.</p></td> + </tr> + <tr> + <th>weibull</th> + <td><p>A boolean defining if the cumulative density curves of weibull distributions + (<code>pweibull</code> with additionall location parameter and scale=1) + are fitted to the decadic logarithm of the dose. Default is FALSE. + Note that the weibull distribution is fitted here to the log transformed doses + which appears to be an uncommon approach.</p></td> + </tr> + <tr> + <th>linlogit</th> + <td><p>A boolean defining if the linear-logistic function + <code><a href='linlogitf.html'>linlogitf</a></code> as defined by van Ewijk and Hoekstra 1993 is + fitted to the data. Default is FALSE.</p></td> + </tr> + <tr> + <th>level</th> + <td><p>The level for the confidence interval listed for the log ED50.</p></td> + </tr> + <tr> + <th>linlogitWrong</th> + <td><p>An optional vector containing the names of the substances for which the + linlogit function produces a wrong fit.</p></td> + </tr> + <tr> + <th>allWrong</th> + <td><p>An optional vector containing the names of the substances for which all + functions produce a wrong fit.</p></td> + </tr> + <tr> + <th>chooseone</th> + <td><p>If TRUE (default), the models are tried in the order linlogit, probit, + logit, weibull, and the first model that produces a valid fit is used. + If FALSE, all models that are set to TRUE and that can be fitted will be + reported.</p></td> + </tr> + <tr> + <th>ps0</th> + <td><p>If the probit model is fitted, <code>ps0</code> gives the possibility to adjust + the starting value for the scale parameter of <code>pnorm</code>.</p></td> + </tr> + <tr> + <th>ls0</th> + <td><p>If the logit model is fitted, <code>ls0</code> gives the possibility to adjust + the starting value for the scale parameter of <code>plogis</code>.</p></td> + </tr> + <tr> + <th>ws0</th> + <td><p>If the weibull model is fitted, <code>ws0</code> gives the possibility to adjust + the starting value for the shape parameter of <code>pweibull</code>.</p></td> + </tr> + <tr> + <th>b0,f0</th> + <td><p>If the linearlogistic model is fitted, <code>b0</code> and <code>f0</code> give the + possibility to adjust the starting values for the parameters b and f.</p></td> + </tr> + <tr> + <th>showED50</th> + <td><p>If set to TRUE, the ED50 and its confidence interval on the original dose + scale (not log scale) is included in the output.</p></td> + </tr> + <tr> + <th>EDx</th> + <td><p>A vector of inhibition values x in percent for which the corresponding doses + EDx should be reported.</p></td> + </tr> + <tr> + <th>EDx.tolerance</th> + <td><p>Tolerance of the effect level, expressed on the response scale from 0 to 1.</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>A dataframe with the attribute <code>models</code> holding a list of the fitted + dose-response models of class <code>nls</code>. The dataframe has at least + one line for each substance.</p> +<p>For the “linlogit”, “logit” and “probit” models, the + 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> +<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> + <dt>lld</dt><dd><p>The decadic logarithm of the lowest dose</p></dd> + <dt>lhd</dt><dd><p>The total number of data points in the raw data used for the fit</p></dd> + <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 + 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. + 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> + <dt>unit</dt><dd><p>The unit used for the dose levels in the dose-response data</p></dd> + <dt>sigma</dt><dd><p>The square root of the estimated variance of the random error as returned + by <code>summary.nls</code>.</p></dd> + <dt>a</dt><dd><p>For the “linlogit”, “logit” and “probit” models, the + parameter <code>a</code> coincides with the logED50. In the case of the + “weibull” model, <code>a</code> is a location parameter.</p></dd> + <dt>b</dt><dd><p>Parameter <code>b</code> in the case of the “linlogit” fit is the variable + b from the <code>linlogitf</code> function. In the case of “probit” + fit it is the standard deviation of the fitted normal distribution, in the + case of the “logit” fit it is the <code>scale</code> parameter in the + <code>plogis</code> function, and in the “weibull” fit it is the + <code>shape</code> parameter of the fitted <code>pweibull</code> function.</p></dd> + <dt>c</dt><dd><p>Only the “linlogit” fit produces a third parameter <code>c</code> which is + the variable f from the <code>linlogitf</code> function.</p></dd> + If the parameter showED50 was set to TRUE, the ED50 values and their + confidence intervals are also included on the original dose scale. + + If one or more response leves were specified in the argument EDx, + the corresponding dose levels are given in addition. + + + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> + + <p>There is a demo for each dataset that can be accessed by + <code>demo(dataset)</code></p> + + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> + + <p>Further examples are given in help pages to the datasets + <code><a href='antifoul.html'>antifoul</a></code>, <code><a href='IM1xIPC81.html'>IM1xIPC81</a></code> and + <code><a href='IM1xVibrio.html'>IM1xVibrio</a></code>. + Since version 0.6.1 of this package, there is a drop-in replacement function + <code><a href='drcfit.html'>drcfit</a></code> which internally uses the drc package and also gives + confidence intervals for EDx values via this package.</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>) +<span class='no'>r</span> <span class='kw'><-</span> <span class='fu'>drfit</span>(<span class='no'>antifoul</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'>format</span>(<span class='no'>r</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma a +#> 1 TBT 38 135 -2.7 2.4 probit -0.16 -0.27 -0.056 microM 0.19 -0.16 +#> 2 Zn Pyrithion 27 81 -2.1 2.0 probit -0.40 -0.51 -0.292 microM 0.23 -0.40 +#> b ED50 ED50 2.5% ED50 97.5% EDx5 EDx10 EDx20 +#> 1 0.68 0.68 0.54 0.88 0.053 0.093 0.18 +#> 2 0.42 0.40 0.31 0.51 0.082 0.117 0.18</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="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#note">Note</a></li> + + <li><a href="#see-also">See also</a></li> + + <li><a href="#examples">Examples</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/drplot.html b/docs/reference/drplot.html new file mode 100644 index 0000000..eff1338 --- /dev/null +++ b/docs/reference/drplot.html @@ -0,0 +1,268 @@ +<!-- 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>Plot dose-response models — drplot • 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> + +<!-- 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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>Plot dose-response models</h1> + </div> + + + <p>Produce graphics of dose-response data and dose-response relationships + either combined or separately, for one or more substances.</p> + + + <pre><span class='fu'>drplot</span>(<span class='no'>drresults</span>, <span class='no'>data</span>, <span class='no'>dtype</span>, <span class='no'>alpha</span>, <span class='no'>ctype</span>, <span class='no'>path</span>, + <span class='no'>fileprefix</span>, <span class='no'>overlay</span>, <span class='no'>xlim</span>, <span class='no'>ylim</span>, <span class='no'>xlab</span>, <span class='no'>ylab</span>, <span class='no'>axes</span>, <span class='no'>frame.plot</span>, <span class='no'>postscript</span>, + <span class='no'>pdf</span>, <span class='no'>png</span>, <span class='no'>bw</span>, <span class='no'>pointsize</span>, <span class='no'>colors</span>, <span class='no'>ltys</span>, <span class='no'>pchs</span>, <span class='no'>devoff</span>, <span class='no'>lpos</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>drresults</th> + <td><p>A data frame as returned from <code><a href='drfit.html'>drfit</a></code>.</p></td> + </tr> + <tr> + <th>data</th> + <td><p>A data frame as returned from <code><a href='drdata.html'>drdata</a></code>. The data frame has to + contain at least a factor called "substance", a vector called "unit" + containing the unit used for the dose, a column "response" with the + response values of the test system normalized between 0 and 1, a column + "dose" with the numeric dose values and a factor called "dosefactor" + containing the dose as a factor.</p></td> + </tr> + <tr> + <th>dtype</th> + <td><p>A string describing if the raw data should be plotted ("raw"), or an error + bar should be constructed from the standard deviations of the responses at + each dose level ("std", default value) or from the confidence intervals + ("conf"). If you don't want to see the data, set it to "none".</p></td> + </tr> + <tr> + <th>alpha</th> + <td><p>The confidence level, defaulting to 0.95, only used if dtype "conf" has been + chosen.</p></td> + </tr> + <tr> + <th>ctype</th> + <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 + interval for the mean of the controls.</p></td> + </tr> + <tr> + <th>path</th> + <td><p>The path where graphic files should be put if any are produced. Defaults + to "./" i.e. the current working directory of R.</p></td> + </tr> + <tr> + <th>fileprefix</th> + <td><p>A string which will form the beginning of each filename, if graphic files + are created. Defaults to "drplot".</p></td> + </tr> + <tr> + <th>overlay</th> + <td><p>If TRUE, all output will be put into one graph, otherwise a separate graph + will be created for each substance.</p></td> + </tr> + <tr> + <th>xlim</th> + <td><p>The plot limits (min,max) on the dose axis.</p></td> + </tr> + <tr> + <th>ylim</th> + <td><p>The plot limits (min,max) on the response axis.</p></td> + </tr> + <tr> + <th>xlab</th> + <td><p>The axis title for the x axis. Defaults to "Concentration in" <code>unit</code>.</p></td> + </tr> + <tr> + <th>ylab</th> + <td><p>The axis title for the y axis. Defaults to "Normalized response".</p></td> + </tr> + <tr> + <th>axes</th> + <td><p>Specifies if axes should be drawn. Default is TRUE, as in + <code>plot.default</code></p></td> + </tr> + <tr> + <th>frame.plot</th> + <td><p>Specifies if the plot should be framed. Default is TRUE, as in + <code>plot.default</code></p></td> + </tr> + <tr> + <th>postscript</th> + <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 + the postscript, and png arguments are also FALSE, graphics will be + displayed with a screen graphics device.</p></td> + </tr> + <tr> + <th>png</th> + <td><p>If TRUE, (a) png graph(s) will be created. Otherwise, and if the + postscript and pdf arguments are also FALSE, graphics will be displayed + with a screen graphics device.</p></td> + </tr> + <tr> + <th>bw</th> + <td><p>A boolean deciding if the plots will be black and white or not. Default + is TRUE.</p></td> + </tr> + <tr> + <th>pointsize</th> + <td><p>The pointsize used for pdf, png and postscript graphics.</p></td> + </tr> + <tr> + <th>colors</th> + <td><p>This is a vector of colors, defaulting to 1:8, used for plotting the data.</p></td> + </tr> + <tr> + <th>ltys</th> + <td><p>This is a vector of line types for the dose-response models, defaulting to 1:8.</p></td> + </tr> + <tr> + <th>pchs</th> + <td><p>This is a vector of character types for the data. The default uses built-in + characters 1:n with n being the number of substances for which data are plotted + for overlays, or always 1 when no overlay plot is generated.</p></td> + </tr> + <tr> + <th>lpos</th> + <td><p>An optional argument defaulting to "topright" specifying the position + of the legend by being passed to the legend function. See the help for the + legend function for all possiblities.</p></td> + </tr> + <tr> + <th>devoff</th> + <td><p>If set to FALSE, the device will not be closed after creation of an overlay + pdf, png or postscript graph, so texts and other elements can + be added.</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p></p> +<dt>results</dt><dd><p>You will get plots of data and/or the fitted dose-response curves, on the + screen and/or as postscript/pdf/png files, depending on the parameters.</p></dd> + + + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> + + <p>There is a demo for each dataset that can be accessed by + <code>demo(dataset)</code></p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>) +<span class='no'>r</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</span>)</div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='co'>## Not run: drplot(r,antifoul)</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="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#note">Note</a></li> + + <li><a href="#examples">Examples</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/index.html b/docs/reference/index.html new file mode 100644 index 0000000..d92d4dc --- /dev/null +++ b/docs/reference/index.html @@ -0,0 +1,195 @@ +<!-- 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>Function reference • drfit</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" 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</div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9"> + <div class="page-header"> + <h1>Function reference</h1> + <h4>version 0.7.1</h4> + </div> + + <div class="contents"> + <table class="ref-index"> + + <colgroup> + <col class="alias" /> + <col class="title" /> + </colgroup> + + <tbody> + <tr> + <th colspan="2"> + <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2> + <p class="section-desc"></p> + </th> + </tr> + <tr> + <!-- --> + <td> + <p><code><a href="antifoul.html">antifoul</a></code> </p> + </td> + <td><p>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="checkcontrols.html">checkcontrols</a></code> </p> + </td> + <td><p>Check raw data from range of plates or experiments</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="checkexperiment.html">checkexperiment</a></code> <code><a href="checkexperiment.html">checkplate</a></code> </p> + </td> + <td><p>Check raw data from a specified experiment or microtiter plate</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="drcfit.html">drcfit</a></code> </p> + </td> + <td><p>Fit dose-response models using the drc package</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="drdata.html">drdata</a></code> </p> + </td> + <td><p>Get dose-response data via RODBC</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="drfit-package.html">drfit-package</a></code> </p> + </td> + <td><p>Dose-response data evaluation</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="drfit.html">drfit</a></code> </p> + </td> + <td><p>Fit dose-response models</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="drplot.html">drplot</a></code> </p> + </td> + <td><p>Plot dose-response models</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="IM1xIPC81.html">IM1xIPC81</a></code> </p> + </td> + <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="IM1xVibrio.html">IM1xVibrio</a></code> </p> + </td> + <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="linlogitf.html">linlogitf</a></code> </p> + </td> + <td><p>Linear-logistic function</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="pyrithione.html">pyrithione</a></code> </p> + </td> + <td><p>Cytotoxicity data for different pyrithionates and related species</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="XY.html">XY</a></code> </p> + </td> + <td><p>Dose-Response data for two substances X and Y</p></td> + </tr> + </tbody> + </table> + </div> + </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="#section-all-functions">All functions</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> |
