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-rw-r--r--DESCRIPTION4
-rw-r--r--R/drplot.R9
-rw-r--r--demo/00Index5
-rw-r--r--demo/IM1xIPC81.R6
-rw-r--r--demo/IM1xVibrio.R6
-rw-r--r--demo/XY.R6
-rw-r--r--demo/antifoul.R5
-rw-r--r--demo/pyrithione.R12
-rw-r--r--man/IM1xIPC81.Rd3
-rw-r--r--man/IM1xVibrio.Rd3
-rw-r--r--man/XY.Rd3
-rw-r--r--man/antifoul.Rd3
-rw-r--r--man/checkexperiment.Rd4
-rw-r--r--man/checksubstance.Rd12
-rw-r--r--man/drdata.Rd46
-rw-r--r--man/drfit-package.Rd8
-rw-r--r--man/drfit.Rd2
-rw-r--r--man/drplot.Rd22
-rw-r--r--man/pyrithione.Rd3
-rw-r--r--tests/IM1xIPC81.R4
-rw-r--r--tests/IM1xIPC81.Rout.save75
-rw-r--r--tests/IM1xVibrio.R4
-rw-r--r--tests/IM1xVibrio.Rout.save57
-rw-r--r--tests/XY.R4
-rw-r--r--tests/XY.Rout.save37
-rw-r--r--tests/antifoul.R4
-rw-r--r--tests/antifoul.Rout.save33
-rw-r--r--tests/pyrithione.R4
-rw-r--r--tests/pyrithione.Rout.save85
29 files changed, 419 insertions, 50 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index f2aee98..b860b9b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: drfit
-Version: 0.05-73
-Date: 2006-04-26
+Version: 0.05-74
+Date: 2006-04-28
Title: Dose-response data evaluation
Author: Johannes Ranke <jranke@uni-bremen.de>
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
diff --git a/R/drplot.R b/R/drplot.R
index eaae85b..e690653 100644
--- a/R/drplot.R
+++ b/R/drplot.R
@@ -7,6 +7,7 @@ drplot <- function(drresults, data,
pointsize = 12,
colors = 1:8, devoff=T, lpos="topright")
{
+ op <- par(no.readonly = TRUE)
# Check if all data have the same unit
unitlevels <- levels(as.factor(drresults$unit))
if (length(unitlevels) == 1) {
@@ -85,9 +86,9 @@ drplot <- function(drresults, data,
ylab = "Normalized response")
} else {
# If overlay plot is not requested, ask before showing multiple plots on the screen
- if (!postscript && !png && !pdf) {
- par(ask=TRUE)
- }
+ if (!postscript && !png && !pdf && length(dsubstances) > 1) {
+ op <- par(ask=TRUE)
+ }
}
# Plot the data either as raw data or as error bars
@@ -219,4 +220,6 @@ drplot <- function(drresults, data,
dev.off()
}
}
+ # Reset the ask parameter to previous setting
+ par(op)
}
diff --git a/demo/00Index b/demo/00Index
new file mode 100644
index 0000000..45b0319
--- /dev/null
+++ b/demo/00Index
@@ -0,0 +1,5 @@
+IM1xIPC81 Analysis of chain methylimidazolium chain length cytotox data
+IM1xVibrio Analysis of chain methylimidazolium chain length V. fischeri data
+XY Analysis of the sample Lemna data called XY
+antifoul Analysis of the cytotoxicity data for TBT and ZnPT
+pyrithione Analysis of the cytotoxicity of pyrithione and related species
diff --git a/demo/IM1xIPC81.R b/demo/IM1xIPC81.R
new file mode 100644
index 0000000..2615a7e
--- /dev/null
+++ b/demo/IM1xIPC81.R
@@ -0,0 +1,6 @@
+require(drfit)
+data(IM1xIPC81)
+rIM1xIPC81 <- drfit(IM1xIPC81,linlogit=TRUE)
+rIM1xIPC81
+drplot(rIM1xIPC81,IM1xIPC81,
+ overlay=TRUE,bw=FALSE,xlim=c("auto",5.5))
diff --git a/demo/IM1xVibrio.R b/demo/IM1xVibrio.R
new file mode 100644
index 0000000..b92a08d
--- /dev/null
+++ b/demo/IM1xVibrio.R
@@ -0,0 +1,6 @@
+require(drfit)
+data(IM1xVibrio)
+rIM1xVibrio <- drfit(IM1xVibrio)
+rIM1xVibrio
+drplot(rIM1xVibrio,IM1xVibrio,
+ overlay=TRUE,bw=FALSE,lpos="bottomleft")
diff --git a/demo/XY.R b/demo/XY.R
new file mode 100644
index 0000000..04a4c5e
--- /dev/null
+++ b/demo/XY.R
@@ -0,0 +1,6 @@
+require(drfit)
+data(XY)
+rXY <- drfit(XY)
+rXY
+drplot(rXY,XY,dtype="raw",
+ overlay=TRUE,bw=FALSE)
diff --git a/demo/antifoul.R b/demo/antifoul.R
new file mode 100644
index 0000000..be63bff
--- /dev/null
+++ b/demo/antifoul.R
@@ -0,0 +1,5 @@
+require(drfit)
+data(antifoul)
+rantifoul <- drfit(antifoul)
+rantifoul
+drplot(rantifoul,antifoul,overlay=TRUE,bw=FALSE)
diff --git a/demo/pyrithione.R b/demo/pyrithione.R
new file mode 100644
index 0000000..5b5a75d
--- /dev/null
+++ b/demo/pyrithione.R
@@ -0,0 +1,12 @@
+require(drfit)
+data(pyrithione)
+
+# MSPT and MSPHI give unreasonable fits with the linlogit model
+rpyr <- drfit(pyrithione,linlogit=TRUE,linlogitWrong=c("MSPT","MSPHI"))
+rpyr
+
+# Consult the above result list to sort out the colors
+drplot(rpyr,pyrithione,dtype="none",overlay=TRUE,bw=FALSE,
+ colors=rainbow(14),xlim=c("auto",8))
+
+drplot(rpyr,pyrithione)
diff --git a/man/IM1xIPC81.Rd b/man/IM1xIPC81.Rd
index 40aaa81..4f5a1dd 100644
--- a/man/IM1xIPC81.Rd
+++ b/man/IM1xIPC81.Rd
@@ -20,6 +20,9 @@
\code{\link{drfit}} function. An additional column contains
the tested organism (name of the cell line).
}
+\examples{
+ \dontrun{demo(IM1xIPC81)}
+}
\source{
Ranke J, M闤ter K, Stock F, Bottin-Weber U, Poczobutt J,
Hoffmann J, Ondruschka B, Filser J, Jastorff B (2004)
diff --git a/man/IM1xVibrio.Rd b/man/IM1xVibrio.Rd
index 454e099..5315432 100644
--- a/man/IM1xVibrio.Rd
+++ b/man/IM1xVibrio.Rd
@@ -18,6 +18,9 @@
Vibrio fischeri, \code{organism}), and a field specifying if the data is
regarded valid (\code{ok}).
}
+\examples{
+ \dontrun{demo(IM1xVibrio)}
+}
\source{
Ranke J, M闤ter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J,
Ondruschka B, Filser J, Jastorff B (2004) Biological effects of imidazolium
diff --git a/man/XY.Rd b/man/XY.Rd
index ab304ba..8022264 100644
--- a/man/XY.Rd
+++ b/man/XY.Rd
@@ -11,6 +11,9 @@
A dataframe containing dose (concentration) and response data, as well as
control values where the dose is zero.
}
+\examples{
+ \dontrun{demo(XY)}
+}
\source{
\url{http://www.uft.uni-bremen.de/chemie}
}
diff --git a/man/antifoul.Rd b/man/antifoul.Rd
index bebec41..2aa532e 100644
--- a/man/antifoul.Rd
+++ b/man/antifoul.Rd
@@ -14,6 +14,9 @@
for TBT and Zink Pyrithione, respectively. Some additional columns from the
database are also present.
}
+\examples{
+ \dontrun{demo(antifoul)}
+}
\source{
\url{http://www.uft.uni-bremen.de/chemie}
}
diff --git a/man/checkexperiment.Rd b/man/checkexperiment.Rd
index d68cd87..56db90c 100644
--- a/man/checkexperiment.Rd
+++ b/man/checkexperiment.Rd
@@ -22,8 +22,8 @@
The function lists a report and shows two graphs side by side.
}
\examples{
-# Check plate number 1 in the cytotox database
-\dontrun{data <- checkplate(3)}
+# Check plate number 3 in the cytotox database
+\dontrun{checkplate(3)}
}
\author{
Johannes Ranke
diff --git a/man/checksubstance.Rd b/man/checksubstance.Rd
index 59759e8..f5340fe 100644
--- a/man/checksubstance.Rd
+++ b/man/checksubstance.Rd
@@ -16,13 +16,15 @@
of the UFT Department of Bioorganic Chemistry are supported (default is
"cytotox").}
\item{experimentator}{
- The name of the experimentator whose data is to be used. Default is "\%", which
- means that data from all experimentators are shown.}
+ The name of the experimentator whose data is to be used. Default is "\%",
+ which means that data from all experimentators are shown.}
\item{celltype}{
- 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.}
+ 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.}
\item{enzymetype}{
- Currently, only data for AChE, GR and GST are supported. The default value is "\%", i.e. data for any enzyme type will be displayed.}
+ Currently, only data for AChE, GR and GST are supported. The default value
+ is "\%", i.e. data for any enzyme type will be displayed.}
\item{whereClause}{
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).}
diff --git a/man/drdata.Rd b/man/drdata.Rd
index 0c1e901..8f545da 100644
--- a/man/drdata.Rd
+++ b/man/drdata.Rd
@@ -1,8 +1,8 @@
\name{drdata}
\alias{drdata}
-\title{Get dose-response data}
+\title{Get dose-response data via RODBC}
\description{
- Get dose-response data from a remote mysql server
+ Get dose-response data from an adequate ODBC data source
}
\usage{
drdata(substances, experimentator = "\%", db = "cytotox", celltype = "IPC-81",
@@ -14,39 +14,40 @@
A string or an array of strings with the substance names for
which dose-response data is to be retrieved.}
\item{experimentator}{
- The name of the experimentator whose data is to be used. Default is "%", which
- means that data from all experimentators are retrieved.}
+ The name of the experimentator whose data is to be used. Default is "%",
+ which means that data from all experimentators are retrieved.}
\item{db}{
- The database to be used. Currently, the databases "cytotox" and "enzymes"
- of the UFT Department of Bioorganic Chemistry are supported (default is
- "cytotox").}
+ The database to be used. Currently, the databases "cytotox", "enzymes"
+ and "ecotox" of the UFT Department of Bioorganic Chemistry are
+ supported (default is "cytotox").}
\item{celltype}{
- Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.}
+ Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are
+ supported.}
\item{enzymetype}{
Currently, only data for AChE, GR and GST are supported.}
\item{organism}{
The organism that was exposed to the chemical. Only important if the database
"ecotox" is used. Defaults to "Vibrio fischeri".}
\item{endpoint}{
- The endpoint that should be used for selecting the data. Only important if the
- database "ecotox" is used. Defaults to "Vibrio fischeri".}
+ The endpoint that should be used for selecting the data. Only important if
+ the database "ecotox" is used. Defaults to "Luminescence".}
\item{whereClause}{
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).}
\item{ok}{
- 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.}
+ 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.}
}
\value{
\item{data}{
- 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.}
+ 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.}
}
\details{
The function is currently only used for retrieving data from the
@@ -74,11 +75,12 @@
Database \tab = \tab cytotox \cr
Server \tab = \tab eckehaat \cr
Port \tab = \tab 3306 \cr
- }.
+ }
}
\examples{
-# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81 cells
-\dontrun{data <- drdata(c("TBT","ZnPT2"))}
+# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81
+# cells
+\dontrun{drdata(c("TBT","ZnPT2"))}
}
\author{
Johannes Ranke
diff --git a/man/drfit-package.Rd b/man/drfit-package.Rd
index d98e10e..43334ff 100644
--- a/man/drfit-package.Rd
+++ b/man/drfit-package.Rd
@@ -13,14 +13,16 @@ There is a preliminary version of an introductory article located in \url{../doc
\author{
Author and Maintainer: Johannes Ranke <jranke@uni-bremen.de>
}
+\note{There is a demo for each dataset that can be accessed by
+ \code{demo(dataset)}}
\keyword{ package }
\keyword{ models }
\keyword{ regression }
\keyword{ nonlinear }
\seealso{
-There is another, more statistically sophisticated package with similar
-functionality called \code{\link[drc:drc-package]{drc}}. I think my package is
-more user-friendly, though.
+On CRAN, there is another, more statistically sophisticated package with
+similar functionality called \code{\link[drc:drc-package]{drc}}. I think
+the advantage of my package is its user-friendliness.
}
\examples{
data(antifoul)
diff --git a/man/drfit.Rd b/man/drfit.Rd
index 9eb5476..a89b5dd 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -100,6 +100,8 @@ data(antifoul)
r <- drfit(antifoul)
format(r,digits=2)
}
+\note{There is a demo for each dataset that can be accessed by
+ \code{demo(dataset)}}
\author{
Johannes Ranke
\email{jranke@uni-bremen.de}
diff --git a/man/drplot.Rd b/man/drplot.Rd
index f8f8aa8..bff2388 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -49,9 +49,7 @@
}
\item{overlay}{
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.
+ will be created for each substance.
}
\item{xlim}{
The plot limits (min,max) on the dose axis.
@@ -66,7 +64,7 @@
}
\item{pdf}{
If TRUE, (a) pdf graph(s) will be created. Otherwise, and if
- the postscript and png arguments are also FALSE, graphics will be
+ the postscript, and png arguments are also FALSE, graphics will be
displayed with a screen graphics device.
}
\item{png}{
@@ -79,7 +77,7 @@
is TRUE.
}
\item{pointsize}{
- The pointsize used for png and postscript graphics.
+ The pointsize used for pdf, png and postscript graphics.
}
\item{colors}{
This is a vector of colors, defaulting to 1:8, used for plotting the data.
@@ -89,26 +87,24 @@
of the legend by being passed to the legend function. See the help for the
legend function for all possiblities.}
\item{devoff}{
- If set to FALSE, the closing of the device after creation of an overlay png
- or postscript graph will be left out, so texts and other elements can be
- added to the graph.
+ 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.
}
}
\value{
\item{results}{
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.
+ screen and/or as postscript/pdf/png files, depending on the parameters.
}
}
-\note{
- Be sure all devices are closed (e.g. by calling \code{dev.off()}) before
- calling \code{drplot} again after a failure.
-}
\examples{
data(antifoul)
r <- drfit(antifoul)
\dontrun{drplot(r,antifoul)}
}
+\note{There is a demo for each dataset that can be accessed by
+ \code{demo(dataset)}}
\author{
Johannes Ranke
\email{jranke@uni-bremen.de}
diff --git a/man/pyrithione.Rd b/man/pyrithione.Rd
index b24a906..f2d3064 100644
--- a/man/pyrithione.Rd
+++ b/man/pyrithione.Rd
@@ -11,6 +11,9 @@
\format{
A dataframe containing the data as required for the \code{\link{drfit}}
function. }
+\examples{
+ \dontrun{demo(pyrithione)}
+}
\source{
Doose C, Ranke J, Stock F, Bottin-Weber U, Jastorff B (2004)
Structure-activity relationships of pyrithiones - IPC-81 toxicity tests with
diff --git a/tests/IM1xIPC81.R b/tests/IM1xIPC81.R
new file mode 100644
index 0000000..075c84d
--- /dev/null
+++ b/tests/IM1xIPC81.R
@@ -0,0 +1,4 @@
+library(drfit)
+data(IM1xIPC81)
+rIM1xIPC81 <- drfit(IM1xIPC81,linlogit=TRUE)
+rIM1xIPC81
diff --git a/tests/IM1xIPC81.Rout.save b/tests/IM1xIPC81.Rout.save
new file mode 100644
index 0000000..b67ed2a
--- /dev/null
+++ b/tests/IM1xIPC81.Rout.save
@@ -0,0 +1,75 @@
+
+R : Copyright 2006, The R Foundation for Statistical Computing
+Version 2.3.0 (2006-04-24)
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(drfit)
+Loading required package: RODBC
+> data(IM1xIPC81)
+> rIM1xIPC81 <- drfit(IM1xIPC81,linlogit=TRUE)
+
+IM13 BF4: Fitting data...
+
+IM14 BF4: Fitting data...
+Error in nls(response ~ linlogitf(dose, 1, f, logED50, b), data = tmp, :
+ singular gradient
+Error in numericDeriv(form[[3]], names(ind), env) :
+ Missing value or an infinity produced when evaluating the model
+In addition: Warning message:
+NaNs produced in: pnorm(q, mean, sd, lower.tail, log.p)
+
+IM15 BF4: Fitting data...
+
+IM16 BF4: Fitting data...
+
+IM17 BF4: Fitting data...
+Error in numericDeriv(form[[3]], names(ind), env) :
+ Missing value or an infinity produced when evaluating the model
+In addition: Warning message:
+NaNs produced in: pnorm(q, mean, sd, lower.tail, log.p)
+
+IM18 BF4: Fitting data...
+Error in numericDeriv(form[[3]], names(ind), env) :
+ Missing value or an infinity produced when evaluating the model
+In addition: Warning message:
+NaNs produced in: pnorm(q, mean, sd, lower.tail, log.p)
+
+IM19 BF4: Fitting data...
+Error in numericDeriv(form[[3]], names(ind), env) :
+ Missing value or an infinity produced when evaluating the model
+In addition: Warning message:
+NaNs produced in: pnorm(q, mean, sd, lower.tail, log.p)
+
+IM1-10 BF4: Fitting data...
+> rIM1xIPC81
+ Substance ndl n lld lhd mtype logED50 std unit
+1 IM13 BF4 9 81 0.59176003 3.000000 inactive NA NA 然
+2 IM14 BF4 20 216 -0.01030017 3.176091 no fit NA NA 然
+3 IM15 BF4 9 135 0.59176003 3.000000 inactive NA NA 然
+4 IM16 BF4 9 108 0.59176003 3.000000 inactive NA NA 然
+5 IM17 BF4 9 81 0.59176003 3.000000 linlogit 2.5785719 0.03819482 然
+6 IM18 BF4 9 135 0.59176003 3.000000 linlogit 1.6806040 0.02982682 然
+7 IM19 BF4 9 81 0.59176003 3.000000 linlogit 1.6496121 0.02636274 然
+8 IM1-10 BF4 11 162 -0.01030017 3.000000 linlogit 0.7696961 0.04165397 然
+ sigma a b c
+1 NA NA NA NA
+2 NA NA NA NA
+3 NA NA NA NA
+4 NA NA NA NA
+5 0.2375857 2.5785719 2.300216 0.01468034
+6 0.2324871 1.6806040 2.237338 0.05719295
+7 0.1452716 1.6496121 1.976976 0.10956088
+8 0.2987708 0.7696961 1.936253 0.45808611
+>
diff --git a/tests/IM1xVibrio.R b/tests/IM1xVibrio.R
new file mode 100644
index 0000000..ed1a698
--- /dev/null
+++ b/tests/IM1xVibrio.R
@@ -0,0 +1,4 @@
+library(drfit)
+data(IM1xVibrio)
+rIM1xVibrio <- drfit(IM1xVibrio)
+rIM1xVibrio
diff --git a/tests/IM1xVibrio.Rout.save b/tests/IM1xVibrio.Rout.save
new file mode 100644
index 0000000..5d37703
--- /dev/null
+++ b/tests/IM1xVibrio.Rout.save
@@ -0,0 +1,57 @@
+
+R : Copyright 2006, The R Foundation for Statistical Computing
+Version 2.3.0 (2006-04-24)
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(drfit)
+Loading required package: RODBC
+> data(IM1xVibrio)
+> rIM1xVibrio <- drfit(IM1xVibrio)
+
+IM13 BF4: Fitting data...
+
+IM14 BF4: Fitting data...
+
+IM15 BF4: Fitting data...
+
+IM16 BF4: Fitting data...
+
+IM17 BF4: Fitting data...
+
+IM18 BF4: Fitting data...
+
+IM19 BF4: Fitting data...
+
+IM1-10 BF4: Fitting data...
+> rIM1xVibrio
+ Substance ndl n lld lhd mtype logED50 std unit
+1 IM13 BF4 13 22 -5.30103 4.69897 probit 3.9399128 0.03658457 然
+2 IM14 BF4 12 57 -4.30103 4.69897 probit 3.5442110 0.02060194 然
+3 IM15 BF4 7 20 -0.30103 4.69897 probit 3.1398488 0.01254468 然
+4 IM16 BF4 13 30 -4.30103 4.69897 probit 3.1804247 0.01801591 然
+5 IM17 BF4 10 20 -1.30103 4.69897 probit 2.4317301 0.03015341 然
+6 IM18 BF4 10 17 -2.30103 2.69897 probit 1.4015187 0.04053083 然
+7 IM19 BF4 13 22 -5.30103 2.69897 probit 0.7157942 0.02085130 然
+8 IM1-10 BF4 11 20 -6.30103 2.69897 probit -0.1790307 0.03623821 然
+ sigma a b
+1 0.06302893 3.9399128 0.5763074
+2 0.05905375 3.5442110 0.6561300
+3 0.02695476 3.1398488 0.5526675
+4 0.04514079 3.1804247 0.4881559
+5 0.04773317 2.4317301 0.6386547
+6 0.05611347 1.4015187 0.8008513
+7 0.02956284 0.7157942 0.6969275
+8 0.04098662 -0.1790307 0.8019351
+>
diff --git a/tests/XY.R b/tests/XY.R
new file mode 100644
index 0000000..e295be4
--- /dev/null
+++ b/tests/XY.R
@@ -0,0 +1,4 @@
+library(drfit)
+data(XY)
+rXY <- drfit(XY)
+rXY
diff --git a/tests/XY.Rout.save b/tests/XY.Rout.save
new file mode 100644
index 0000000..7bcc0df
--- /dev/null
+++ b/tests/XY.Rout.save
@@ -0,0 +1,37 @@
+
+R : Copyright 2006, The R Foundation for Statistical Computing
+Version 2.3.0 (2006-04-24)
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(drfit)
+Loading required package: RODBC
+> data(XY)
+> rXY <- drfit(XY)
+
+Control: Fitting data...
+
+Substance X: Fitting data...
+
+Substance Y: Fitting data...
+> rXY
+ Substance ndl n lld lhd mtype logED50 std unit sigma
+1 Control 1 6 -Inf -Inf inactive NA NA mg/L NA
+2 Substance X 4 12 1 3 probit 2.161905 0.02425144 mg/L 0.04131746
+3 Substance Y 4 12 1 3 active NA NA mg/L NA
+ a b
+1 NA NA
+2 2.161905 0.5061306
+3 NA NA
+>
diff --git a/tests/antifoul.R b/tests/antifoul.R
new file mode 100644
index 0000000..f9c1a9d
--- /dev/null
+++ b/tests/antifoul.R
@@ -0,0 +1,4 @@
+library(drfit)
+data(antifoul)
+rantifoul <- drfit(antifoul)
+rantifoul
diff --git a/tests/antifoul.Rout.save b/tests/antifoul.Rout.save
new file mode 100644
index 0000000..5bc166c
--- /dev/null
+++ b/tests/antifoul.Rout.save
@@ -0,0 +1,33 @@
+
+R : Copyright 2006, The R Foundation for Statistical Computing
+Version 2.3.0 (2006-04-24)
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(drfit)
+Loading required package: RODBC
+> data(antifoul)
+> rantifoul <- drfit(antifoul)
+
+TBT: Fitting data...
+
+Zn Pyrithion: Fitting data...
+> rantifoul
+ Substance ndl n lld lhd mtype logED50 std unit
+1 TBT 38 135 -2.709271 2.39794 probit -0.1643560 0.05349216 然
+2 Zn Pyrithion 27 81 -2.107210 2.00000 probit -0.3979222 0.05393693 然
+ sigma a b
+1 0.1928611 -0.1643560 0.6763882
+2 0.2286560 -0.3979222 0.4169632
+>
diff --git a/tests/pyrithione.R b/tests/pyrithione.R
new file mode 100644
index 0000000..f05988d
--- /dev/null
+++ b/tests/pyrithione.R
@@ -0,0 +1,4 @@
+library(drfit)
+data(pyrithione)
+rpyr <- drfit(pyrithione,linlogit=TRUE,linlogitWrong=c("MSPT","MSPHI"))
+rpyr
diff --git a/tests/pyrithione.Rout.save b/tests/pyrithione.Rout.save
new file mode 100644
index 0000000..fb11ca9
--- /dev/null
+++ b/tests/pyrithione.Rout.save
@@ -0,0 +1,85 @@
+
+R : Copyright 2006, The R Foundation for Statistical Computing
+Version 2.3.0 (2006-04-24)
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(drfit)
+Loading required package: RODBC
+> data(pyrithione)
+> rpyr <- drfit(pyrithione,linlogit=TRUE,linlogitWrong=c("MSPT","MSPHI"))
+
+Na Pyrithion: Fitting data...
+
+Pyridin: Fitting data...
+
+PyNO: Fitting data...
+
+(PT)2: Fitting data...
+
+MSO2P: Fitting data...
+
+MSPHI: Fitting data...
+
+PyS: Fitting data...
+Error in nls(response ~ linlogitf(dose, 1, f, logED50, b), data = tmp, :
+ step factor 0.000488281 reduced below 'minFactor' of 0.000976562
+
+Zn Pyrithion: Fitting data...
+
+Cu Pyrithion: Fitting data...
+
+Fe Pyrithion: Fitting data...
+
+(PyS)2: Fitting data...
+Error in nls(response ~ linlogitf(dose, 1, f, logED50, b), data = tmp, :
+ singular gradient
+
+MSPT: Fitting data...
+
+TBT: Fitting data...
+
+NaJ: Fitting data...
+> rpyr
+ Substance ndl n lld lhd mtype logED50 std unit
+1 Na Pyrithion 20 108 -2.107210 2.00000 linlogit -0.3461318 0.04237833 然
+2 Pyridin 19 161 0.591760 3.69897 inactive NA NA 然
+3 PyNO 19 81 0.591760 3.69897 no fit NA NA 然
+4 (PT)2 19 81 -2.408240 2.00000 linlogit -0.4197031 0.05030460 然
+5 MSO2P 28 108 -1.709271 3.69897 inactive NA NA 然
+6 MSPHI 19 81 0.591760 3.69897 probit 3.6625025 0.06724673 然
+7 PyS 18 80 -0.408240 3.00000 probit 2.6817944 0.02031252 然
+8 Zn Pyrithion 27 81 -2.107210 2.00000 linlogit -0.4132885 0.06234927 然
+9 Cu Pyrithion 19 79 -2.408240 2.00000 linlogit -0.3074717 0.07918130 然
+10 Fe Pyrithion 19 81 -2.408240 2.00000 linlogit -0.3534572 0.07263386 然
+11 (PyS)2 20 81 -0.408240 3.00000 probit 1.7840499 0.05230663 然
+12 MSPT 18 108 -0.408240 3.00000 probit 2.1384811 0.03379904 然
+13 TBT 38 135 -2.709271 2.39794 linlogit -0.1580954 0.05474371 然
+14 NaJ 10 108 0.591760 3.30103 inactive NA NA 然
+ sigma a b c
+1 0.20857751 -0.3461318 2.1188272 -0.26698979
+2 NA NA NA NA
+3 0.09188853 NA NA NA
+4 0.20509070 -0.4197031 1.8466994 -0.51508088
+5 NA NA NA NA
+6 0.12943273 3.6625025 0.4387540 NA
+7 0.13401920 2.6817944 0.1250523 NA
+8 0.22877916 -0.4132885 1.7424846 0.61078660
+9 0.24494451 -0.3074717 1.0150649 -0.04897422
+10 0.23383185 -0.3534572 1.1823558 0.02510613
+11 0.23298721 1.7840499 0.4098018 NA
+12 0.22881257 2.1384811 0.2112625 NA
+13 0.19264079 -0.1580954 1.0406576 -0.02416104
+14 NA NA NA NA
+>

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