- Fixed the drplot function, so the graphics parameter ask is adequately set

  depending on the overlay argument, and set back to the previous value
- Added a test for each datase
- Added a demo for each dataset
- Corrected many small bugs in the documentation and improved formatting
  of the .Rd files



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@74 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

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
+>