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-rw-r--r--DESCRIPTION2
-rw-r--r--R/drfit.R88
-rw-r--r--chm/00Index.html28
-rw-r--r--chm/Rchm.css25
-rw-r--r--chm/antifoul.html49
-rwxr-xr-xchm/checkplate.html68
-rw-r--r--chm/drdata.html147
-rw-r--r--chm/drfit.chmbin30423 -> 0 bytes
-rw-r--r--chm/drfit.hhp18
-rw-r--r--chm/drfit.html99
-rw-r--r--chm/drfit.toc59
-rw-r--r--chm/drplot.html143
-rw-r--r--chm/logo.jpgbin8793 -> 0 bytes
-rw-r--r--man/drfit.Rd12
-rwxr-xr-xman/linlogitf.Rd2
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
Binary files differ
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
Binary files differ
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.}
}

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