Add checkcontrols, updates, see ChangeLog

13 files changed, 76 insertions, 76 deletions

diff --git a/man/IM1xIPC81.Rd b/man/IM1xIPC81.Rd
index dda0c3b..5994f6a 100644
--- a/man/IM1xIPC81.Rd
+++ b/man/IM1xIPC81.Rd
@@ -29,7 +29,7 @@
   print(rIM1xIPC81.drc,digits=4)
 }
 \source{
-  Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J,
+  Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J,
   Hoffmann J, Ondruschka B, Filser J, Jastorff B (2004)
   Biological effects of imidazolium ionic liquids with varying
   chain lenghts in acute Vibrio fischeri and WST-1 cell
diff --git a/man/IM1xVibrio.Rd b/man/IM1xVibrio.Rd
index cb0bd48..d3258fb 100644
--- a/man/IM1xVibrio.Rd
+++ b/man/IM1xVibrio.Rd
@@ -6,9 +6,9 @@
   This is the raw data documenting the influence of the alkyl chain length in 3
   position on the toxicity to the marine luminescent bacteria \emph{V.
   fischeri}. The substances are named according to the UFT naming scheme of
-  these substances. 
-  IM13 BF4 means 1-methyl-3-propylimidazolium tetrafluoroborate, 
-  IM14 BF4 means 1-methyl-3-butylimidazolium tetrafluoroborate and 
+  these substances.
+  IM13 BF4 means 1-methyl-3-propylimidazolium tetrafluoroborate,
+  IM14 BF4 means 1-methyl-3-butylimidazolium tetrafluoroborate and
   IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate.
 }
 \usage{data(IM1xVibrio)}
@@ -28,7 +28,7 @@
   print(rIM1xVibrio.drc, digits = 4)
 }
 \source{
-  Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J,
+  Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J,
   Ondruschka B, Filser J, Jastorff B (2004) Biological effects of imidazolium
   ionic liquids with varying chain lenghts in acute Vibrio fischeri and WST-1
   cell viability assays. Ecotoxicology and Environmental Safety 58(3) 396-404
diff --git a/man/XY.Rd b/man/XY.Rd
index 8022264..82a48fe 100644
--- a/man/XY.Rd
+++ b/man/XY.Rd
@@ -3,7 +3,7 @@
 \alias{XY}
 \title{Dose-Response data for two substances X and Y}
 \description{
-  This is just a sample Lemna growth rate data set for two substances 
+  This is just a sample Lemna growth rate data set for two substances
   arbitrarily named X and Y.
 }
 \usage{data(XY)}
diff --git a/man/antifoul.Rd b/man/antifoul.Rd
index 21ae885..e782636 100644
--- a/man/antifoul.Rd
+++ b/man/antifoul.Rd
@@ -3,9 +3,9 @@
 \alias{antifoul}
 \title{Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells}
 \description{
-  This data set shows the response of the rat leukaemic cell line IPC-81 to 
+  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 
+  from the "cytotox" database of the UFT Department of Bioorganic Chemistry on
   February 25, 2004
 }
 \usage{data(antifoul)}
@@ -15,15 +15,15 @@
   database are also present.
 }
 \examples{
-rantifoul.ED50 <- drfit(antifoul, 
+rantifoul.ED50 <- drfit(antifoul,
                         linlogit = TRUE, logit = TRUE, weibull = TRUE,
-                        chooseone = FALSE, 
+                        chooseone = FALSE,
                         showED50 = TRUE, EDx = c(10))
 print(rantifoul.ED50, digits = 5)
 
-rantifoul.drc <- drcfit(antifoul, 
+rantifoul.drc <- drcfit(antifoul,
                         linlogit = TRUE, logit = TRUE, weibull = TRUE,
-                        chooseone = FALSE, 
+                        chooseone = FALSE,
                         showED50 = TRUE, EDx = c(10))
 print(rantifoul.drc, digits = 5)
 }
diff --git a/man/checkcontrols.Rd b/man/checkcontrols.Rd
index b155643..3941a69 100644
--- a/man/checkcontrols.Rd
+++ b/man/checkcontrols.Rd
@@ -6,7 +6,7 @@
   experiments from a specified database.
 }
 \usage{
-  checkcontrols(last = 10, id = NULL, db = "cytotox", organism = "Vibrio fischeri", 
+  checkcontrols(last = 10, id = NULL, db = "cytotox", organism = "Vibrio fischeri",
                 endpoint = "\%", qcc = c("R", "xbar"))
 }
 \arguments{
@@ -29,9 +29,9 @@
     The endpoint that should be used for selecting the data. Only important if
     the database "ecotox" is used. Defaults to "\%".}
   \item{qcc}{
-    The type of quality control charts to be plotted. By default, an R chart 
-    (showing ranges of control values within plates/experiments), and an 
-    xbar chart (showing means) are generated. 
+    The type of quality control charts to be plotted. By default, an R chart
+    (showing ranges of control values within plates/experiments), and an
+    xbar chart (showing means) are generated.
   }
 }
 \value{
@@ -41,8 +41,8 @@
 \dontrun{checkcontrols(15)}
 }
 \author{
-  Johannes Ranke 
-  \email{jranke@uni-bremen.de} 
+  Johannes Ranke
+  \email{jranke@uni-bremen.de}
   \url{http://www.uft.uni-bremen.de/chemie/ranke}
 }
 \keyword{database}
diff --git a/man/checkexperiment.Rd b/man/checkexperiment.Rd
index 0edf2fb..6a682fa 100644
--- a/man/checkexperiment.Rd
+++ b/man/checkexperiment.Rd
@@ -29,8 +29,8 @@
 \dontrun{checkplate(3)}
 }
 \author{
-  Johannes Ranke 
-  \email{jranke@uni-bremen.de} 
+  Johannes Ranke
+  \email{jranke@uni-bremen.de}
   \url{http://www.uft.uni-bremen.de/chemie/ranke}
 }
 \keyword{database}
diff --git a/man/checksubstance.Rd b/man/checksubstance.Rd
index 387785f..6182fce 100644
--- a/man/checksubstance.Rd
+++ b/man/checksubstance.Rd
@@ -6,8 +6,8 @@
   the data.
 }
 \usage{
-  checksubstance(substance, db = "cytotox", experimentator = "\%", 
-    celltype = "\%", enzymetype = "\%", organism = "\%", 
+  checksubstance(substance, db = "cytotox", experimentator = "\%",
+    celltype = "\%", enzymetype = "\%", organism = "\%",
     endpoint = "\%",
     whereClause = "1", ok = "\%")
 }
@@ -17,7 +17,7 @@
   \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").} 
+    "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.}
@@ -35,10 +35,10 @@
     The endpoint that should be used for selecting the data. Only important if
     the database "ecotox" is used. Defaults to "\%".}
   \item{whereClause}{
-    With this argument, additional conditions for the SQL query can be set, 
+    With this argument, additional conditions for the SQL query can be set,
     e.g. "plate != 710". The default is 1 (in SQL syntax this means TRUE).}
   \item{ok}{
-    With the default value "\%", all data in the database is retrieved for the 
+    With the default value "\%", all data in the database is retrieved for the
     specified substance.}
 }
 \value{
@@ -49,8 +49,8 @@
 \dontrun{checksubstance("IM14 BF4")}
 }
 \author{
-  Johannes Ranke 
-  \email{jranke@uni-bremen.de} 
+  Johannes Ranke
+  \email{jranke@uni-bremen.de}
   \url{http://www.uft.uni-bremen.de/chemie/ranke}
 }
 \keyword{database}
diff --git a/man/drcfit.Rd b/man/drcfit.Rd
index b10418a..67462ba 100644
--- a/man/drcfit.Rd
+++ b/man/drcfit.Rd
@@ -7,7 +7,7 @@
 }
 \usage{
   drcfit(data, chooseone = TRUE, probit = TRUE, logit = FALSE,
-  weibull = FALSE, linlogit = FALSE, level = 0.95, 
+  weibull = FALSE, linlogit = FALSE, level = 0.95,
   showED50 = FALSE, EDx = NULL)
 }
 \arguments{
@@ -67,7 +67,7 @@
 \value{
   A dataframe with the attribute \code{models} holding a list of the fitted
   dose-response models of class \code{\link{nls}}. The dataframe has at least
-  one line for each substance. 
+  one line for each substance.
 
   The following variables are in the dataframe:
   \item{Substance}{
@@ -89,14 +89,14 @@
     If the data did not show a mean response < 0.5 at the highest dose level,
     the modeltype is set to \dQuote{inactive}. If the mean response at the
     lowest dose is smaller than 0.5, the modeltype is set to \dQuote{active}.
-    In both cases, no fitting procedure is carried out. If the fitted ED50 
+    In both cases, no fitting procedure is carried out. If the fitted ED50
     is higher than the highest dose, \dQuote{no fit} is given here.
   }
   \item{logED50}{
     The decadic logarithm of the ED50
   }
   \item{low \%}{
-    The lower bound of the confidence interval of log ED50. 
+    The lower bound of the confidence interval of log ED50.
     The name of the column depends on the requested confidence \code{level}.
   }
   \item{high \%}{
@@ -112,16 +112,16 @@
   }
   \item{a}{
     For the linlogit model, this is the parameter e from \code{\link{BC.4}}.
-    For the probit and the logit model, this is the ED50. For the weibull 
-    model, this is parameter e from \code{\link{W1.2}}. Note that the Weibull 
+    For the probit and the logit model, this is the ED50. For the weibull
+    model, this is parameter e from \code{\link{W1.2}}. Note that the Weibull
     model is fitted to the untransformed data.
   }
   \item{b}{
     For the linlogit, probit, logit and weibull models, these are the
-    parameters b from \code{\link{BC.4}}, \code{\link{LN.2}}, 
+    parameters b from \code{\link{BC.4}}, \code{\link{LN.2}},
     \code{\link{LL.2}} and \code{\link{W1.2}}, respectively.
     Note that the parameter definitions (and in the case of Weibull, the model
-    used) are different to the ones used in \code{\link{drfit}}. 
+    used) are different to the ones used in \code{\link{drfit}}.
   }
   \item{c}{
     Only the \dQuote{linlogit} fit produces a third parameter \code{c}, which is
@@ -140,14 +140,14 @@ r <- drcfit(antifoul, showED50 = TRUE, EDx = c(5, 10, 20))
 format(r, digits = 2)
 }
 \note{There is a demo for each dataset that can be accessed by
-  \code{demo(dataset)}} 
+  \code{demo(dataset)}}
 \seealso{
   Further examples are given in help pages to the datasets
   \code{\link{antifoul}}, \code{\link{IM1xIPC81}} and
   \code{\link{IM1xVibrio}}.
 }
 \author{
-  Johannes Ranke \email{jranke@uni-bremen.de} 
+  Johannes Ranke \email{jranke@uni-bremen.de}
   \url{http://www.uft.uni-bremen.de/chemie/ranke}
   The functionality of the drc package used under the hood in this function
   was written by Christian Ritz.
diff --git a/man/drdata.Rd b/man/drdata.Rd
index 8f545da..4fb6740 100644
--- a/man/drdata.Rd
+++ b/man/drdata.Rd
@@ -2,11 +2,11 @@
 \alias{drdata}
 \title{Get dose-response data via RODBC}
 \description{
-	Get dose-response data from an adequate ODBC data source
+  Get dose-response data from an adequate ODBC data source
 }
 \usage{
-  drdata(substances, experimentator = "\%", db = "cytotox", celltype = "IPC-81", 
-    enzymetype="AChE", organism="Vibrio fischeri", endpoint="Luminescence", 
+  drdata(substances, experimentator = "\%", db = "cytotox", celltype = "IPC-81",
+    enzymetype="AChE", organism="Vibrio fischeri", endpoint="Luminescence",
     whereClause = "1", ok = "'ok','no fit'")
 }
 \arguments{
@@ -18,11 +18,11 @@
     which means that data from all experimentators are retrieved.}
   \item{db}{
     The database to be used. Currently, the databases "cytotox", "enzymes"
-    and "ecotox" of the UFT Department of Bioorganic Chemistry are 
-    supported (default is "cytotox").} 
+    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.} 
+    supported.}
   \item{enzymetype}{
     Currently, only data for AChE, GR and GST are supported.}
   \item{organism}{
@@ -32,9 +32,9 @@
     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, 
+    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).} 
+    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"
@@ -58,7 +58,7 @@
   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 \file{/etc/odbcinst.ini}
-  containing: 
+  containing:
   \tabular{lll}{
     [MySQL] \tab \tab \cr
     Description \tab = \tab MySQL driver for ODBC \cr
@@ -83,8 +83,8 @@
 \dontrun{drdata(c("TBT","ZnPT2"))}
 }
 \author{
-  Johannes Ranke 
-  \email{jranke@uni-bremen.de} 
+  Johannes Ranke
+  \email{jranke@uni-bremen.de}
   \url{http://www.uft.uni-bremen.de/chemie/ranke}
 }
 \keyword{IO}
diff --git a/man/drfit-package.Rd b/man/drfit-package.Rd
index 696cee9..06a147f 100644
--- a/man/drfit-package.Rd
+++ b/man/drfit-package.Rd
@@ -16,7 +16,7 @@ of R for chemists.
 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)}} 
+  \code{demo(dataset)}}
 \keyword{ package }
 \keyword{ models }
 \keyword{ regression }
diff --git a/man/drfit.Rd b/man/drfit.Rd
index 3729550..ec7fa70 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -9,7 +9,7 @@
   drfit(data, startlogED50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE,
   weibull = FALSE, linlogit = FALSE, level = 0.95, linlogitWrong = NA,
   allWrong = NA, ps0 = 1, ls0 = 0.5, ws0 = 0.5, b0 = 2, f0 = 0,
-  showED50 = FALSE, 
+  showED50 = FALSE,
   EDx = NULL, EDx.tolerance = 1e-4)
 }
 \arguments{
@@ -32,11 +32,11 @@
   \item{probit}{
     A boolean defining if cumulative density curves of normal distributions
     \code{\link{pnorm}} are fitted against the decadic logarithm of the dose.
-    Default ist TRUE.} 
+    Default ist TRUE.}
   \item{logit}{
     A boolean defining if cumulative density curves of logistic distributions
     \code{\link{plogis}} are fitted to the decadic logarithm of the dose.
-    Default is FALSE.} 
+    Default is FALSE.}
   \item{weibull}{
     A boolean defining if the cumulative density curves of weibull distributions
     (\code{\link{pweibull}} with additionall location parameter and scale=1)
@@ -87,14 +87,14 @@
 \value{
   A dataframe with the attribute \code{models} holding a list of the fitted
   dose-response models of class \code{\link{nls}}. The dataframe has at least
-  one line for each substance. 
+  one line for each substance.
 
   For the \dQuote{linlogit}, \dQuote{logit} and \dQuote{probit} models, the
   parameter \code{a} that is reported coincides with the logED50, i.e the
   logED50 is one of the model parameters that is being fitted. Therefore,
   a confidence interval for the confidence level \code{level} is calculated
   using the \code{\link[MASS:confint]{confint.nls}} function and listed.
-  
+
   The following variables are in the dataframe:
   \item{Substance}{
     The name of the substance
@@ -115,14 +115,14 @@
     If the data did not show a mean response < 0.5 at the highest dose level,
     the modeltype is set to \dQuote{inactive}. If the mean response at the
     lowest dose is smaller than 0.5, the modeltype is set to \dQuote{active}.
-    In both cases, no fitting procedure is carried out. If the fitted ED50 
+    In both cases, no fitting procedure is carried out. If the fitted ED50
     is higher than the highest dose, \dQuote{no fit} is given here.
   }
   \item{logED50}{
     The decadic logarithm of the ED50
   }
   \item{low \%}{
-    The lower bound of the confidence interval of log ED50. 
+    The lower bound of the confidence interval of log ED50.
     The name of the column depends on the requested confidence \code{level}.
   }
   \item{high \%}{
@@ -139,7 +139,7 @@
   \item{a}{
     For the \dQuote{linlogit}, \dQuote{logit} and \dQuote{probit} models, the
     parameter \code{a} coincides with the logED50.  In the case of the
-    \dQuote{weibull} model, \code{a} is a location parameter. 
+    \dQuote{weibull} model, \code{a} is a location parameter.
   }
   \item{b}{
     Parameter \code{b} in the case of the \dQuote{linlogit} fit is the variable
@@ -165,7 +165,7 @@ r <- drfit(antifoul, showED50 = TRUE, EDx = c(5, 10, 20))
 format(r, digits = 2)
 }
 \note{There is a demo for each dataset that can be accessed by
-  \code{demo(dataset)}} 
+  \code{demo(dataset)}}
 \seealso{
   Further examples are given in help pages to the datasets
   \code{\link{antifoul}}, \code{\link{IM1xIPC81}} and
@@ -175,8 +175,8 @@ format(r, digits = 2)
   confidence intervals for EDx values via this package.
 }
 \author{
-  Johannes Ranke 
-  \email{jranke@uni-bremen.de} 
+  Johannes Ranke
+  \email{jranke@uni-bremen.de}
   \url{http://www.uft.uni-bremen.de/chemie/ranke}
 }
 \keyword{models}
diff --git a/man/drplot.Rd b/man/drplot.Rd
index e9e4dd1..6b8a7bf 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -2,7 +2,7 @@
 \alias{drplot}
 \title{Plot dose-response models}
 \description{
-  Produce graphics of dose-response data and dose-response relationships 
+  Produce graphics of dose-response data and dose-response relationships
   either combined or separately, for one or more substances.
 }
 \usage{
@@ -14,13 +14,13 @@
   \item{drresults}{
     A data frame as returned from \code{\link{drfit}}.
     }
-  \item{data}{ 
+  \item{data}{
     A data frame as returned from \code{\link{drdata}}. 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. 
+    containing the dose as a factor.
     }
   \item{dtype}{
     A string describing if the raw data should be plotted ("raw"), or an error
@@ -33,7 +33,7 @@
     chosen.
     }
   \item{ctype}{
-    This argument decides if horizontal lines are drawn to show the scatter of 
+    This argument decides if horizontal lines are drawn to show the scatter of
     the control values (dose = 0), if there are more than three of them.
     Defaults to "none", further allowed values are "std" and "conf" for
     displaying the standard deviation of the controls or the confidence
@@ -49,7 +49,7 @@
     }
   \item{overlay}{
     If TRUE, all output will be put into one graph, otherwise a separate graph
-    will be created for each substance. 
+    will be created for each substance.
     }
   \item{xlim}{
     The plot limits (min,max) on the dose axis.
@@ -72,12 +72,12 @@
     \code{\link{plot.default}}
   }
   \item{postscript}{
-    If TRUE, (a) postscript graph(s) will be created. Otherwise, and if 
+    If TRUE, (a) postscript graph(s) will be created. Otherwise, and if
     the pdf and png arguments are also FALSE, graphics will be
     displayed with a screen graphics device.
     }
   \item{pdf}{
-    If TRUE, (a) pdf graph(s) will be created. Otherwise, and if 
+    If TRUE, (a) pdf graph(s) will be created. Otherwise, and if
     the postscript, and png arguments are also FALSE, graphics will be
     displayed with a screen graphics device.
     }
@@ -87,7 +87,7 @@
     with a screen graphics device.
     }
   \item{bw}{
-    A boolean deciding if the plots will be black and white or not. Default 
+    A boolean deciding if the plots will be black and white or not. Default
     is TRUE.
     }
   \item{pointsize}{
@@ -107,7 +107,7 @@
   \item{lpos}{
     An optional argument defaulting to "topright" specifying the position
     of the legend by being passed to the legend function. See the help for the
-    legend function for all possiblities.} 
+    legend function for all possiblities.}
   \item{devoff}{
     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
@@ -119,17 +119,17 @@
     You will get plots of data and/or the fitted dose-response curves, on the
     screen and/or as postscript/pdf/png files, depending on the parameters.
     }
-} 
+}
 \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)}} 
+  \code{demo(dataset)}}
 \author{
-  Johannes Ranke 
-  \email{jranke@uni-bremen.de} 
+  Johannes Ranke
+  \email{jranke@uni-bremen.de}
   \url{http://www.uft.uni-bremen.de/chemie/ranke}
 }
 \keyword{models}
diff --git a/man/linlogitf.Rd b/man/linlogitf.Rd
index f091581..2c9ddc4 100755..100644
--- a/man/linlogitf.Rd
+++ b/man/linlogitf.Rd
@@ -22,13 +22,13 @@
 }
 \value{
   The response at dose x.
-} 
+}
 \references{
   van Ewijk, P. H. and Hoekstra, J. A. (1993) \emph{Ecotox Environ Safety}
   \bold{25} 25-32}
 \author{
-  Johannes Ranke 
-  \email{jranke@uni-bremen.de} 
+  Johannes Ranke
+  \email{jranke@uni-bremen.de}
   \url{http://www.uft.uni-bremen.de/chemie/ranke}
 }
 \keyword{models}