Changed the terminology from EC50 to ED50 reflecting that the package is meant

for dose-response analysis in general and not only for concentration-response
analysis. This is the first revision that has been prepared with the knowledge
of the existence of the drc package for dose-response curve analysis.



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@48 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

15 files changed, 52 insertions, 688 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 87a1302..e5f1e99 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -14,7 +14,7 @@ Description: drfit provides basic functions for fitting dose-response curves to
 	which is used to describe data showing stimulation at low doses
 	(hormesis). 
 	In addition, functions checking, plotting and retrieving dose-response data
-	of the UFT Bremen are provided.
+	retrieved from a database accessed via RODBC are included.
 	I would be delighted if you would join in this effort of creating useful
 	and useable tools for dealing with dose-response data from biological
 	testing.
diff --git a/R/drfit.R b/R/drfit.R
index d8631e6..e74667d 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -44,7 +44,7 @@ linlogitf <- function(x,k,f,mu,b)
     k*(1 + f*x) / (1 + ((2*f*(10^mu) + 1) * ((x/(10^mu))^b)))
 }
 
-drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
+drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
         probit = TRUE, logit = FALSE, weibull = FALSE,
         linlogit = FALSE, linlogitWrong = NA, allWrong = NA,
         s0 = 0.5, b0 = 2, f0 = 0)
@@ -62,8 +62,8 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
     rlhd <- rlld <- vector()              # highest and lowest doses tested
     mtype <- array()                      # the modeltypes
     sigma <- array()                      # the standard deviation of the residuals
-    logEC50 <- vector()
-    stderrlogEC50 <- vector()
+    logED50 <- vector()
+    stderrlogED50 <- vector()
     a <- b <- c <- vector()
 
     splitted <- split(data,data$substance)
@@ -89,9 +89,9 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
         }
         rix <- ri
         if (!nodata) {
-            if (is.na(startlogEC50[i])){
+            if (is.na(startlogED50[i])){
                 w <- 1/abs(tmp$response - 0.3)
-                startlogEC50[[i]] <- sum(w * log10(tmp$dose))/sum(w)
+                startlogED50[[i]] <- sum(w * log10(tmp$dose))/sum(w)
             }
             highestdose <- max(tmp$dose)
             lowestdose <- min(tmp$dose)
@@ -104,9 +104,9 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                 if (linlogit && 
                     length(subset(linlogitWrong,linlogitWrong == i))==0 &&
                     length(subset(allWrong,allWrong == i))==0) {
-                    m <- try(nls(response ~ linlogitf(dose,1,f,logEC50,b),
+                    m <- try(nls(response ~ linlogitf(dose,1,f,logED50,b),
                             data=tmp,
-                            start=list(f=f0,logEC50=startlogEC50[[i]],b=b0)))
+                            start=list(f=f0,logED50=startlogED50[[i]],b=b0)))
                     if (!inherits(m, "try-error")) {
                         fit <- TRUE
                         ri <- ri + 1
@@ -117,18 +117,18 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                         runit[[ri]] <- unit
                         rlld[[ri]] <- log10(lowestdose)
                         rlhd[[ri]] <- log10(highestdose)
-                        logEC50[[ri]] <- coef(m)[["logEC50"]]
-                        if (logEC50[[ri]] > rlhd[[ri]]) {
+                        logED50[[ri]] <- coef(m)[["logED50"]]
+                        if (logED50[[ri]] > rlhd[[ri]]) {
                             mtype[[ri]] <- "no fit"
-                            logEC50[[ri]] <- NA
-                            stderrlogEC50[[ri]] <- NA
+                            logED50[[ri]] <- NA
+                            stderrlogED50[[ri]] <- NA
                             a[[ri]] <- NA
                             b[[ri]] <- NA
                             c[[ri]] <- NA
                         } else {
                             mtype[[ri]] <- "linlogit"
-                            stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]
-                            a[[ri]] <- coef(m)[["logEC50"]]
+                            stderrlogED50[[ri]] <- s$parameters["logED50","Std. Error"]
+                            a[[ri]] <- coef(m)[["logED50"]]
                             b[[ri]] <- coef(m)[["b"]]
                             c[[ri]] <- coef(m)[["f"]]
                         }
@@ -137,9 +137,9 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
 
                 if (probit &&
                     length(subset(allWrong,allWrong == i))==0) {
-                    m <- try(nls(response ~ pnorm(-log10(dose),-logEC50,scale),
+                    m <- try(nls(response ~ pnorm(-log10(dose),-logED50,scale),
                                 data=tmp,
-                                start=list(logEC50=startlogEC50[[i]],scale=1)))
+                                start=list(logED50=startlogED50[[i]],scale=1)))
                     if (chooseone==FALSE || fit==FALSE) {
                         if (!inherits(m, "try-error")) {
                             fit <- TRUE
@@ -151,18 +151,18 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                             runit[[ri]] <- unit
                             rlld[[ri]] <- log10(lowestdose)
                             rlhd[[ri]] <- log10(highestdose)
-                            logEC50[[ri]] <- coef(m)[["logEC50"]]
+                            logED50[[ri]] <- coef(m)[["logED50"]]
                             c[[ri]] <- NA
-                            if (logEC50[[ri]] > rlhd[[ri]]) {
+                            if (logED50[[ri]] > rlhd[[ri]]) {
                                 mtype[[ri]] <- "no fit"
-                                logEC50[[ri]] <- NA
-                                stderrlogEC50[[ri]] <- NA
+                                logED50[[ri]] <- NA
+                                stderrlogED50[[ri]] <- NA
                                 a[[ri]] <- NA
                                 b[[ri]] <- NA
                             } else {
                                 mtype[[ri]] <- "probit"
-                                stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]
-                                a[[ri]] <- coef(m)[["logEC50"]]
+                                stderrlogED50[[ri]] <- s$parameters["logED50","Std. Error"]
+                                a[[ri]] <- coef(m)[["logED50"]]
                                 b[[ri]] <- coef(m)[["scale"]]
                             }
                         }
@@ -171,9 +171,9 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
 
                 if (logit &&
                     length(subset(allWrong,allWrong == i))==0) {
-                    m <- try(nls(response ~ plogis(-log10(dose),-logEC50,scale),
+                    m <- try(nls(response ~ plogis(-log10(dose),-logED50,scale),
                             data=tmp,
-                            start=list(logEC50=startlogEC50[[i]],scale=1)))
+                            start=list(logED50=startlogED50[[i]],scale=1)))
                     if (chooseone==FALSE || fit==FALSE) {
                         if (!inherits(m, "try-error")) {
                             fit <- TRUE
@@ -185,18 +185,18 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                             runit[[ri]] <- unit
                             rlld[[ri]] <- log10(lowestdose)
                             rlhd[[ri]] <- log10(highestdose)
-                            logEC50[[ri]] <- a[[ri]] <- coef(m)[["logEC50"]]
+                            logED50[[ri]] <- a[[ri]] <- coef(m)[["logED50"]]
                             b[[ri]] <- coef(m)[["scale"]]
                             c[[ri]] <- NA
-                            if (logEC50[[ri]] > rlhd[[ri]]) {
+                            if (logED50[[ri]] > rlhd[[ri]]) {
                                 mtype[[ri]] <- "no fit"
-                                logEC50[[ri]] <- NA
-                                stderrlogEC50[[ri]] <- NA
+                                logED50[[ri]] <- NA
+                                stderrlogED50[[ri]] <- NA
                                 a[[ri]] <- NA
                                 b[[ri]] <- NA
                             } else {
                                 mtype[[ri]] <- "logit"
-                                stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]
+                                stderrlogED50[[ri]] <- s$parameters["logED50","Std. Error"]
                             }
                         }
                     }
@@ -206,7 +206,7 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                     length(subset(allWrong,allWrong == i))==0) {
                     m <- try(nls(response ~ pweibull(-log10(dose)+location,shape),
                             data=tmp,
-                            start=list(location=startlogEC50[[i]],shape=s0)))
+                            start=list(location=startlogED50[[i]],shape=s0)))
                     if (chooseone==FALSE || fit==FALSE) {
                         if (!inherits(m, "try-error")) {
                             fit <- TRUE
@@ -223,17 +223,17 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                             sqrdev <- function(logdose) {
                                 (0.5 - pweibull( - logdose + a[[ri]], b[[ri]]))^2 
                             }
-                            logEC50[[ri]] <- nlm(sqrdev,startlogEC50[[i]])$estimate
+                            logED50[[ri]] <- nlm(sqrdev,startlogED50[[i]])$estimate
                             c[[ri]] <- NA
-                            if (logEC50[[ri]] > rlhd[[ri]]) {
+                            if (logED50[[ri]] > rlhd[[ri]]) {
                                 mtype[[ri]] <- "no fit"
-                                logEC50[[ri]] <- NA
-                                stderrlogEC50[[ri]] <- NA
+                                logED50[[ri]] <- NA
+                                stderrlogED50[[ri]] <- NA
                                 a[[ri]] <- NA
                                 b[[ri]] <- NA
                             } else {
                                 mtype[[ri]] <- "weibull"
-                                stderrlogEC50[[ri]] <- NA
+                                stderrlogED50[[ri]] <- NA
                             }
                         }
                     }
@@ -263,15 +263,15 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                 }
             }
             sigma[[ri]] <- NA
-            logEC50[[ri]] <- NA
-            stderrlogEC50[[ri]] <- NA
+            logED50[[ri]] <- NA
+            stderrlogED50[[ri]] <- NA
             a[[ri]] <- NA
             b[[ri]] <- NA
             c[[ri]] <- NA
         }
     }
-    results <- data.frame(rsubstance, rn, rlld, rlhd, mtype, logEC50, stderrlogEC50, runit, sigma, a, b)
-    names(results) <- c("Substance","n","lld","lhd","mtype","logEC50","std","unit","sigma","a","b")
+    results <- data.frame(rsubstance, rn, rlld, rlhd, mtype, logED50, stderrlogED50, runit, sigma, a, b)
+    names(results) <- c("Substance","n","lld","lhd","mtype","logED50","std","unit","sigma","a","b")
     if (linlogit) {
         results$c <- c
     }
@@ -303,8 +303,8 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95,
         hr <- max(data$response)
         dsubstances <- levels(data$substance)    
     } else {
-        lld <- min(drresults[["logEC50"]],na.rm=TRUE) - 2
-        lhd <- max(drresults[["logEC50"]],na.rm=TRUE) + 2
+        lld <- min(drresults[["logED50"]],na.rm=TRUE) - 2
+        lhd <- max(drresults[["logED50"]],na.rm=TRUE) + 2
         if (length(subset(drresults,mtype=="linlogit")$Substance) != 0) {
             hr <- 1.8 
         } else {
@@ -419,15 +419,15 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95,
                 if (nf > 0) {
                     for (j in 1:nf)
                     {
-                        logEC50 <- fits[j,"logEC50"]
+                        logED50 <- fits[j,"logED50"]
                         mtype <- as.character(fits[j, "mtype"])
                         if (mtype == "probit") {
                             scale <- fits[j,"b"]
-                            plot(function(x) pnorm(-x,-logEC50,scale),lld - 0.5, lhd + 2, add=TRUE,col=color)
+                            plot(function(x) pnorm(-x,-logED50,scale),lld - 0.5, lhd + 2, add=TRUE,col=color)
                         }
                         if (mtype == "logit") {
                             scale <- fits[j,"b"]
-                            plot(function(x) plogis(-x,-logEC50,scale),lld - 0.5, lhd + 2, add=TRUE,col=color)
+                            plot(function(x) plogis(-x,-logED50,scale),lld - 0.5, lhd + 2, add=TRUE,col=color)
                         }
                         if (mtype == "weibull") {
                             location <- fits[j,"a"]
@@ -435,7 +435,7 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95,
                             plot(function(x) pweibull(-x+location,shape),lld - 0.5, lhd + 2, add=TRUE,col=color)
                         }
                         if (mtype == "linlogit") {
-                            plot(function(x) linlogitf(10^x,1,fits[j,"c"],fits[j,"logEC50"],fits[j,"b"]),
+                            plot(function(x) linlogitf(10^x,1,fits[j,"c"],fits[j,"logED50"],fits[j,"b"]),
                                 lld - 0.5, lhd + 2,
                                 add=TRUE,col=color)
                         }
diff --git a/chm/00Index.html b/chm/00Index.html
deleted file mode 100644
index 066b05a..0000000
--- a/chm/00Index.html
+++ /dev/null
@@ -1,28 +0,0 @@
-<html><head><title>Dose-response data evaluation</title>

-<link rel="stylesheet" type="text/css" href="Rchm.css">

-</head><body>

-<h1>Dose-response data evaluation

-<img class="toplogo" src="logo.jpg" alt="[R logo]"></h1>

-

-<hr>

-

-<object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">

-<param name="keyword" value=".. contents">

-</object>

-

-<h2>Help pages for package `drfit' version 0.03-9</h2>

-

-

-<table width="100%">

-<tr><td width="25%"><a href="antifoul.html">antifoul</a></td>

-<td>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</td></tr>

-<tr><td width="25%"><a href="checkplate.html">checkplate</a></td>

-<td>Check raw data from a specified microtiter plate</td></tr>

-<tr><td width="25%"><a href="drdata.html">drdata</a></td>

-<td>Get dose-response data</td></tr>

-<tr><td width="25%"><a href="drfit.html">drfit</a></td>

-<td>Fit dose-response models</td></tr>

-<tr><td width="25%"><a href="drplot.html">drplot</a></td>

-<td>Plot dose-response models</td></tr>

-</table>

-</body></html>

diff --git a/chm/Rchm.css b/chm/Rchm.css
deleted file mode 100644
index badd579..0000000
--- a/chm/Rchm.css
+++ /dev/null
@@ -1,25 +0,0 @@
-BODY{		background: white;
-		color: black }
-
-A:link{         background: white;
-                color: blue }
-A:visited{	background: white;
-		color: rgb(50%, 0%, 50%) }
-
-H1{		background: white;
-		color: rgb(55%, 55%, 55%);
-		font-family: monospace;
-		font-size: large;
-		text-align: center }
-
-H2{		background: white;
-		color: rgb(0%, 0%, 100%);
-		font-family: monospace;
-		text-align: center }
-
-H3{		background: white;
-		color: rgb(40%, 40%, 40%);
-		font-family: monospace }
-
-IMG.toplogo{	vertical-align: middle }
-
diff --git a/chm/antifoul.html b/chm/antifoul.html
deleted file mode 100644
index 810c5e9..0000000
--- a/chm/antifoul.html
+++ /dev/null
@@ -1,49 +0,0 @@
-<html><head><title>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</title>

-<link rel="stylesheet" type="text/css" href="Rchm.css">

-</head>

-<body>

-

-<table width="100%"><tr><td>antifoul(drfit)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">

-<param name="keyword" value="R:   antifoul">

-<param name="keyword" value=" Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells">

-</object>

-

-

-<h2>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</h2>

-

-

-<h3>Description</h3>

-

-<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>

-

-

-<h3>Usage</h3>

-

-<pre>data(antifoul)</pre>

-

-

-<h3>Format</h3>

-

-<p>

-A dataframe containing 135 and 81 data points for concentrations and responses

-for TBT and Zink Pyrithione, respectively. Additional data from the database is 

-also present.

-</p>

-

-

-<h3>Source</h3>

-

-<p>

-<a href="http://www.uft.uni-bremen.de/chemie">http://www.uft.uni-bremen.de/chemie</a>

-</p>

-

-

-

-<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>

-

-</body></html>

diff --git a/chm/checkplate.html b/chm/checkplate.html
deleted file mode 100755
index d545656..0000000
--- a/chm/checkplate.html
+++ /dev/null
@@ -1,68 +0,0 @@
-<html><head><title>Check raw data from a specified microtiter plate</title>

-<link rel="stylesheet" type="text/css" href="Rchm.css">

-</head>

-<body>

-

-<table width="100%"><tr><td>checkplate(drfit)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">

-<param name="keyword" value="R:   checkplate">

-<param name="keyword" value=" Check raw data from a specified microtiter plate">

-</object>

-

-

-<h2>Check raw data from a specified microtiter plate</h2>

-

-

-<h3>Description</h3>

-

-<p>

-Report metadata from a specified microtiter plate from a specified database, box 

-plot positive and negative (blind) controls, and show the response data on the 

-plate.

-</p>

-

-

-<h3>Usage</h3>

-

-<pre>

-  checkplate(plate,db="cytotox")

-</pre>

-

-

-<h3>Arguments</h3>

-

-<table summary="R argblock">

-<tr valign="top"><td><code>plate</code></td>

-<td>

-The number of the plate identifying it within the database.</td></tr>

-<tr valign="top"><td><code>db</code></td>

-<td>

-The database to be used. Currently only "cytotox" of the UFT Department of

-Bioorganic Chemistry is supported.</td></tr>

-</table>

-

-<h3>Value</h3>

-

-<p>

-The function lists a report and shows two graphs.</p>

-

-<h3>Author(s)</h3>

-

-<p>

-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>

-</p>

-

-

-<h3>Examples</h3>

-

-<pre>

-# Check plate number 1 in the cytotox database

-## Not run: data &lt;- checkplate(1)

-</pre>

-

-

-

-<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>

-

-</body></html>

diff --git a/chm/drdata.html b/chm/drdata.html
deleted file mode 100644
index a2ef9d9..0000000
--- a/chm/drdata.html
+++ /dev/null
@@ -1,147 +0,0 @@
-<html><head><title>Get dose-response data</title>

-<link rel="stylesheet" type="text/css" href="Rchm.css">

-</head>

-<body>

-

-<table width="100%"><tr><td>drdata(drfit)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">

-<param name="keyword" value="R:   drdata">

-<param name="keyword" value=" Get dose-response data">

-</object>

-

-

-<h2>Get dose-response data</h2>

-

-

-<h3>Description</h3>

-

-<p>

-Get dose-response data from a remote mysql server

-</p>

-

-

-<h3>Usage</h3>

-

-<pre>

-  drdata(substances, experimentator = "%", db = "cytotox", celltype = "IPC-81", 

-    whereClause = "1", ok = "'ok'")

-</pre>

-

-

-<h3>Arguments</h3>

-

-<table summary="R argblock">

-<tr valign="top"><td><code>substances</code></td>

-<td>

-A string or an array of strings with the substance names for

-which dose-response data is to be retrieved.</td></tr>

-<tr valign="top"><td><code>experimentator</code></td>

-<td>

-The name of the experimentator whose data is to be used.</td></tr>

-<tr valign="top"><td><code>db</code></td>

-<td>

-The database to be used. Currently only "cytotox" of the UFT Department of

-Bioorganic Chemistry is supported.</td></tr>

-<tr valign="top"><td><code>celltype</code></td>

-<td>

-Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.</td></tr>

-<tr valign="top"><td><code>whereClause</code></td>

-<td>

-With this argument, additional conditions for the SQL query can be set, 

-e.g. "where plate != 710". The default is 1 (in SQL syntax this means TRUE).</td></tr>

-<tr valign="top"><td><code>ok</code></td>

-<td>

-With the default value "'ok'", only data that has been checked and set to "ok"

-in the database is retrieved. Another sensible argument would be "'ok','?'", in 

-order to additionally retrieve data which has not yet been checked.</td></tr>

-</table>

-

-<h3>Details</h3>

-

-<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 &lsquo;<TT>/etc/odbcinst.ini</TT>&rsquo;

-containing: 

-<table summary="Rd table">

-<tr>

-  <td align="left">[MySQL] </td>  <td align="left"> </td>  <td align="left"> </td>

-</tr>

-<tr>

-  <td align="left"> Description </td>  <td align="left"> = </td>  <td align="left"> MySQL driver for ODBC </td>

-</tr>

-<tr>

-  <td align="left"> Driver </td>  <td align="left"> = </td>  <td align="left"> /usr/local/lib/libmyodbc.so </td>

-</tr>

-<tr>

-  <td align="left"> Setup </td>  <td align="left"> = </td>  <td align="left"> /usr/lib/odbc/libodbcmyS.so </td>

-</tr>

-</table>

-<p>

-and the file &lsquo;<TT>/etc/odbc.ini</TT>&rsquo; containing:

-<table summary="Rd table">

-<tr>

-  <td align="left">[cytotox] </td>  <td align="left"> </td>  <td align="left"> </td>

-</tr>

-<tr>

-  <td align="left"> Description </td>  <td align="left"> = </td>  <td align="left"> Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen </td>

-</tr>

-<tr>

-  <td align="left"> Driver </td>  <td align="left"> = </td>  <td align="left"> MySQL </td>

-</tr>

-<tr>

-  <td align="left"> Trace </td>  <td align="left"> = </td>  <td align="left"> Yes  </td>

-</tr>

-<tr>

-  <td align="left"> TraceFile </td>  <td align="left"> = </td>  <td align="left"> /tmp/odbc.log  </td>

-</tr>

-<tr>

-  <td align="left"> Database </td>  <td align="left"> = </td>  <td align="left"> cytotox  </td>

-</tr>

-<tr>

-  <td align="left"> Server </td>  <td align="left"> = </td>  <td align="left"> eckehaat  </td>

-</tr>

-<tr>

-  <td align="left"> Port </td>  <td align="left"> = </td>  <td align="left"> 3306  </td>

-</tr>

-</table>

-.

-</p>

-

-

-<h3>Value</h3>

-

-<table summary="R argblock">

-<tr valign="top"><td><code>data</code></td>

-<td>

-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.</td></tr>

-</table>

-

-<h3>Author(s)</h3>

-

-<p>

-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>

-</p>

-

-

-<h3>Examples</h3>

-

-<pre>

-# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81 cells

-## Not run: data &lt;- drdata(c("TBT","Zn Pyrithion"))

-</pre>

-

-

-

-<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>

-

-</body></html>

diff --git a/chm/drfit.chm b/chm/drfit.chm
deleted file mode 100644
index d88cbb3..0000000
--- a/chm/drfit.chm
+++ /dev/null
diff --git a/chm/drfit.hhp b/chm/drfit.hhp
deleted file mode 100644
index 40a9b74..0000000
--- a/chm/drfit.hhp
+++ /dev/null
@@ -1,18 +0,0 @@
-[OPTIONS]

-Auto Index=Yes

-Contents file=drfit.toc

-Compatibility=1.1 or later

-Compiled file=drfit.chm

-Default topic=00Index.html

-Display compile progress=No

-Full-text search=Yes

-Full text search stop list file=..\..\..\gnuwin32\help\R.stp

-

-

-[FILES]

-00Index.html

-antifoul.html

-checkplate.html

-drdata.html

-drfit.html

-drplot.html

diff --git a/chm/drfit.html b/chm/drfit.html
deleted file mode 100644
index 23dd70f..0000000
--- a/chm/drfit.html
+++ /dev/null
@@ -1,99 +0,0 @@
-<html><head><title>Fit dose-response models</title>

-<link rel="stylesheet" type="text/css" href="Rchm.css">

-</head>

-<body>

-

-<table width="100%"><tr><td>drfit(drfit)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">

-<param name="keyword" value="R:   drfit">

-<param name="keyword" value=" Fit dose-response models">

-</object>

-

-

-<h2>Fit dose-response models</h2>

-

-

-<h3>Description</h3>

-

-<p>

-Fit dose-response relationships to dose-response data and calculate

-biometric results for (eco)toxicity evaluation

-</p>

-

-

-<h3>Usage</h3>

-

-<pre>

-  drfit(data, startlogEC50 = NA, lognorm = TRUE, logis = FALSE, 

-    linearlogis = FALSE, b0 = 2, f0 = 0)

-</pre>

-

-

-<h3>Arguments</h3>

-

-<table summary="R argblock">

-<tr valign="top"><td><code>data</code></td>

-<td>

-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 and a column

-"dose" with the numeric dose values. For later use of the

-<code><a href="drplot.html">drplot</a></code> function, a factor called "dosefactor" also has to be

-present, containing the dose as a factor.

-</td></tr>

-<tr valign="top"><td><code>startlogEC50</code></td>

-<td>

-Especially for the linearlogis model, a suitable log10 of the EC50 has to be given 

-by the user, since it is not correctly estimated for data showing hormesis with

-the default estimation method.</td></tr>

-<tr valign="top"><td><code>lognorm</code></td>

-<td>

-A boolean defining if cumulative density curves of normal distributions

-are fitted to the data. Default ist TRUE.</td></tr>

-<tr valign="top"><td><code>logis</code></td>

-<td>

-A boolean defining if cumulative densitiy curves of logistic distributions

-are fitted to the data. Default is FALSE.</td></tr>

-<tr valign="top"><td><code>linearlogis</code></td>

-<td>

-A boolean defining if the linear-logistic function as defined by van Ewijk and Hoekstra

-1993 is fitted to the data. Default is FALSE.</td></tr>

-<tr valign="top"><td><code>b0,f0</code></td>

-<td>

-If the linearlogistic model is fitted, b0 and f0 give the possibility to

-adapt the starting values for the parameters b and f.</td></tr>

-</table>

-

-<h3>Value</h3>

-

-<table summary="R argblock">

-<tr valign="top"><td><code>results</code></td>

-<td>

-A data frame containing at least one line for each substance. If the data did not

-show a mean response &lt; 0.5 at the highest dose level, the modeltype is set to "none".

-Every successful fit is reported in one line. Parameters of the fitted curves are only

-reported if the fitted EC50 is not higher than the highest dose.</td></tr>

-</table>

-

-<h3>Author(s)</h3>

-

-<p>

-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>

-</p>

-

-

-<h3>Examples</h3>

-

-<pre>

-data(antifoul)

-r &lt;- drfit(antifoul)

-format(r,digits=2)

-</pre>

-

-

-

-<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>

-

-</body></html>

diff --git a/chm/drfit.toc b/chm/drfit.toc
deleted file mode 100644
index e80cc53..0000000
--- a/chm/drfit.toc
+++ /dev/null
@@ -1,59 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">

-<HEAD></HEAD><HTML><BODY>

-<UL>

-<LI> <OBJECT type="text/sitemap">

-<param name="Name" value="Package drfit:  Contents">

-<param name="Local" value="00Index.html">

-</OBJECT>

-<LI> <OBJECT type="text/sitemap">

-<param name="Name" value="Package drfit:  R objects">

-</OBJECT>

-<UL>

-<LI> <OBJECT type="text/sitemap">

-<param name="Name" value="antifoul">

-<param name="Local" value="antifoul.html">

-</OBJECT>

-<LI> <OBJECT type="text/sitemap">

-<param name="Name" value="checkplate">

-<param name="Local" value="checkplate.html">

-</OBJECT>

-<LI> <OBJECT type="text/sitemap">

-<param name="Name" value="drdata">

-<param name="Local" value="drdata.html">

-</OBJECT>

-<LI> <OBJECT type="text/sitemap">

-<param name="Name" value="drfit">

-<param name="Local" value="drfit.html">

-</OBJECT>

-<LI> <OBJECT type="text/sitemap">

-<param name="Name" value="drplot">

-<param name="Local" value="drplot.html">

-</OBJECT>

-</UL>

-<LI> <OBJECT type="text/sitemap">

-<param name="Name" value="Package drfit:  Titles">

-</OBJECT>

-<UL>

-<LI> <OBJECT type="text/sitemap">

-<param name="Name" value="Check raw data from a specified microtiter plate">

-<param name="Local" value="checkplate.html">

-</OBJECT>

-<LI> <OBJECT type="text/sitemap">

-<param name="Name" value="Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells">

-<param name="Local" value="antifoul.html">

-</OBJECT>

-<LI> <OBJECT type="text/sitemap">

-<param name="Name" value="Fit dose-response models">

-<param name="Local" value="drfit.html">

-</OBJECT>

-<LI> <OBJECT type="text/sitemap">

-<param name="Name" value="Get dose-response data">

-<param name="Local" value="drdata.html">

-</OBJECT>

-<LI> <OBJECT type="text/sitemap">

-<param name="Name" value="Plot dose-response models">

-<param name="Local" value="drplot.html">

-</OBJECT>

-</UL>

-</UL>

-</BODY></HTML>

diff --git a/chm/drplot.html b/chm/drplot.html
deleted file mode 100644
index 84cf12e..0000000
--- a/chm/drplot.html
+++ /dev/null
@@ -1,143 +0,0 @@
-<html><head><title>Plot dose-response models</title>

-<link rel="stylesheet" type="text/css" href="Rchm.css">

-</head>

-<body>

-

-<table width="100%"><tr><td>drplot(drfit)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">

-<param name="keyword" value="R:   drplot">

-<param name="keyword" value=" Plot dose-response models">

-</object>

-

-

-<h2>Plot dose-response models</h2>

-

-

-<h3>Description</h3>

-

-<p>

-Produce graphics of dose-response data and dose-response relationships 

-either combined or separately, for one or more substances.

-</p>

-

-

-<h3>Usage</h3>

-

-<pre>

-  drplot(drresults, data, dtype, alpha, path, fileprefix, overlay,

-    postscript, color, datacolors, fitcolors)

-</pre>

-

-

-<h3>Arguments</h3>

-

-<table summary="R argblock">

-<tr valign="top"><td><code>drresults</code></td>

-<td>

-A data frame as returned from <code><a href="drfit.html">drfit</a></code>.

-</td></tr>

-<tr valign="top"><td><code>data</code></td>

-<td>

-A data frame as returned from <code><a href="drdata.html">drdata</a></code>.  If data is to be

-plotted, 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. If plotting of the data is 

-not required, data can be set to FALSE.

-</td></tr>

-<tr valign="top"><td><code>dtype</code></td>

-<td>

-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"). Of course, dtype only makes a difference, if a valid data

-object has been referenced.

-</td></tr>

-<tr valign="top"><td><code>alpha</code></td>

-<td>

-The confidence level, defaulting to 0.95, only used if dtype "conf" has been

-chosen.

-</td></tr>

-<tr valign="top"><td><code>path</code></td>

-<td>

-The path where graphic files should be put if any are produced. Defaults

-to "./" i.e. the current working directory of R.

-</td></tr>

-<tr valign="top"><td><code>fileprefix</code></td>

-<td>

-A string which will form the beginning of each filename, if graphic files are 

-created. Defaults to "drplot".

-</td></tr>

-<tr valign="top"><td><code>overlay</code></td>

-<td>

-If TRUE, all output will be put into one graph, otherwise a separate graph

-will be created for each substance. In the latter case, on-screen display

-(postscript=FALSE) only works correctly for data plots. Dose-response models

-will all be put into the last graph in this case.

-</td></tr>

-<tr valign="top"><td><code>postscript</code></td>

-<td>

-If TRUE, (a) postscript graph(s) will be created. Otherwise, graphics will be

-displayed with a screen graphics device.

-</td></tr>

-<tr valign="top"><td><code>color</code></td>

-<td>

-If TRUE, a sensible selection of colors will be attempted. If false, everything

-will be drawn in black

-</td></tr>

-<tr valign="top"><td><code>datacolors</code></td>

-<td>

-This is a vector of colors, defaulting to 1:8, used for plotting the data.

-</td></tr>

-<tr valign="top"><td><code>fitcolors</code></td>

-<td>

-Here you can specify a palette for the colors of the dose-response fits. The 

-default value is "default", which produces the default palette, if the 

-number of fits to be plotted is 8 or less. Otherwise, rainbow colors 

-will be plotted. Unless there is more than one fit per substance to be plotted,

-or the number of fits is larger than 8, the fitcolors will match the

-datacolors.

-</td></tr>

-</table>

-

-<h3>Value</h3>

-

-<table summary="R argblock">

-<tr valign="top"><td><code>results</code></td>

-<td>

-You will get plots of data and/or the fitted dose-response curves, on the

-screen and/or as postscript files, depending on the parameters.

-</td></tr>

-</table>

-

-<h3>Note</h3>

-

-<p>

-Turn off the colors if you don't like them and don't want to fiddle with

-them. Treatment of legends is quite bad. Be sure all devices are closed

-(e.g. by calling <code>dev.off()</code>) before calling <code>drplot</code> again.

-</p>

-

-

-<h3>Author(s)</h3>

-

-<p>

-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>

-</p>

-

-

-<h3>Examples</h3>

-

-<pre>

-data(antifoul)

-r &lt;- drfit(antifoul)

-## Not run: drplot(r,antifoul)

-</pre>

-

-

-

-<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>

-

-</body></html>

diff --git a/chm/logo.jpg b/chm/logo.jpg
deleted file mode 100644
index b8e2149..0000000
--- a/chm/logo.jpg
+++ /dev/null
diff --git a/man/drfit.Rd b/man/drfit.Rd
index 75f48ed..295965d 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -6,7 +6,7 @@
   biometric results for (eco)toxicity evaluation
 }
 \usage{
-  drfit(data, startlogEC50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE,
+  drfit(data, startlogED50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE,
     weibull = FALSE, linlogit = FALSE, linlogitWrong = NA, allWrong = NA, 
     s0 = 0.5, b0 = 2, f0 = 0)
 }
@@ -24,8 +24,8 @@
     line, then the corresponding data point will be excluded from the fitting
     procedure, although it will be plotted.
     }
-  \item{startlogEC50}{
-    Especially for the linlogit model, a suitable log10 of the EC50 has to be given 
+  \item{startlogED50}{
+    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.}
   \item{probit}{
@@ -68,15 +68,15 @@
       did not show a mean response < 0.5 at the highest dose level, the
       modeltype is set to "none".
       Every successful fit is reported in one line. Parameters of the fitted
-      curves are only reported if the fitted EC50 is not higher than the
+      curves are only reported if the fitted ED50 is not higher than the
       highest dose. 
       \code{n} is the number of dose-response curves in the raw data (repetitions
       in each point), \code{lld} is the decadic logarithm of the lowest dose and
       \code{lhd} is the decadic logarithm of the highest dose.
       For the "linlogit", "logit" and "probit" models, the parameter
-      \code{a} that is reported coincides with the logEC50, i.e the logEC50 is 
+      \code{a} that is reported coincides with the logED50, i.e the logED50 is 
       one of the model parameters that is being fitted, and therefore
-      a standard deviation \code{std} is reported for the logEC50. In the 
+      a standard deviation \code{std} is reported for the logED50. In the 
       case of the "weibull" model, \code{a} is a location parameter.
       Parameter \code{b} in the case of the "linlogit" fit is the variable
       b from the \code{\link{linlogitf}} function. In the case of "probit" fit
diff --git a/man/linlogitf.Rd b/man/linlogitf.Rd
index 2eca8c4..f091581 100755
--- a/man/linlogitf.Rd
+++ b/man/linlogitf.Rd
@@ -16,7 +16,7 @@
   \item{f}{
     One of the parameters describing the curve shape.}
   \item{mu}{
-    The parameter describing the location of the curve (log EC50).}
+    The parameter describing the location of the curve (log ED50).}
   \item{b}{
     One of the parameters describing the curve shape.}
 }