diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/IM1xIPC81.Rd | 7 | ||||
| -rw-r--r-- | man/IM1xVibrio.Rd | 8 | ||||
| -rw-r--r-- | man/antifoul.Rd | 13 | ||||
| -rw-r--r-- | man/drcfit.Rd | 110 | ||||
| -rw-r--r-- | man/drfit.Rd | 8 | ||||
| -rw-r--r-- | man/drplot.Rd | 7 |
6 files changed, 149 insertions, 4 deletions
diff --git a/man/IM1xIPC81.Rd b/man/IM1xIPC81.Rd index 4f5a1dd..dda0c3b 100644 --- a/man/IM1xIPC81.Rd +++ b/man/IM1xIPC81.Rd @@ -21,7 +21,12 @@ the tested organism (name of the cell line). } \examples{ - \dontrun{demo(IM1xIPC81)} + rIM1xIPC81 <- drfit(IM1xIPC81, linlogit = TRUE, showED50 = TRUE, EDx = 10) + + rIM1xIPC81.drc <- drcfit(IM1xIPC81, linlogit = TRUE, showED50 = TRUE, EDx = 10) + + print(rIM1xIPC81,digits=4) + print(rIM1xIPC81.drc,digits=4) } \source{ Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, diff --git a/man/IM1xVibrio.Rd b/man/IM1xVibrio.Rd index 5315432..cb0bd48 100644 --- a/man/IM1xVibrio.Rd +++ b/man/IM1xVibrio.Rd @@ -19,7 +19,13 @@ regarded valid (\code{ok}). } \examples{ - \dontrun{demo(IM1xVibrio)} + rIM1xVibrio <- drfit(IM1xVibrio, logit = TRUE, chooseone = FALSE, + showED50 = TRUE, EDx = c(10, 20)) + print(rIM1xVibrio, digits = 4) + + rIM1xVibrio.drc <- drcfit(IM1xVibrio, logit = TRUE, chooseone = FALSE, + showED50 = TRUE, EDx = c(10, 20)) + print(rIM1xVibrio.drc, digits = 4) } \source{ Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J, diff --git a/man/antifoul.Rd b/man/antifoul.Rd index 2aa532e..21ae885 100644 --- a/man/antifoul.Rd +++ b/man/antifoul.Rd @@ -15,8 +15,19 @@ database are also present. } \examples{ - \dontrun{demo(antifoul)} +rantifoul.ED50 <- drfit(antifoul, + linlogit = TRUE, logit = TRUE, weibull = TRUE, + chooseone = FALSE, + showED50 = TRUE, EDx = c(10)) +print(rantifoul.ED50, digits = 5) + +rantifoul.drc <- drcfit(antifoul, + linlogit = TRUE, logit = TRUE, weibull = TRUE, + chooseone = FALSE, + showED50 = TRUE, EDx = c(10)) +print(rantifoul.drc, digits = 5) } + \source{ \url{http://www.uft.uni-bremen.de/chemie} } diff --git a/man/drcfit.Rd b/man/drcfit.Rd new file mode 100644 index 0000000..2da0418 --- /dev/null +++ b/man/drcfit.Rd @@ -0,0 +1,110 @@ +\name{drcfit} +\alias{drcfit} +\title{Fit dose-response models using the drc package} +\description{ + Fit dose-response relationships to dose-response data and calculate + biometric results for (eco)toxicity evaluation using the drc package +} +\usage{ + drcfit(data, chooseone = TRUE, probit = TRUE, logit = FALSE, + weibull = FALSE, linlogit = FALSE, level = 0.95, + showED50 = FALSE, EDx = NULL) +} +\arguments{ + \item{data}{ + A data frame containing dose-response data. The data frame has to contain + at least a factor called \dQuote{substance}, a numeric vector \dQuote{dose} + with the dose values, a vector called \dQuote{unit} containing the unit + used for the dose and a numeric vector \dQuote{response} with the response + values of the test system normalized between 0 and 1. Such a data frame can + be easily obtained if a compliant RODBC data source is available for use in + conjunction with the function \code{\link{drdata}}. + + If there is a column called \dQuote{ok} and it is set to \dQuote{no fit} in + a specific line, then the corresponding data point will be excluded from + the fitting procedure, although it will be plotted.} + \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. + Note that the parameter definitions used in the model are different to the + ones used in \code{\link{drfit}}. Parameter e from \code{\link{LN.2}} is listed + as a here, and parameter b from LN.2 is listed as b.} + \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. + Again the parameter definitions used in the model are different to the + ones used in \code{\link{drfit}}. Parameter e from \code{\link{LL.2}} is listed + as a here, and parameter b from LL.2 is listed as b.} + \item{weibull}{ + A boolean defining if Weibull dose-response models + (\code{\link{W1.2}} are fitted to the untransformed dose. Default is FALSE. + Note that the results differ from the ones obtained with + \code{\link{drfit}}, due to a different model specification.} + \item{linlogit}{ + A boolean defining if the linear-logistic function + \code{\link{linlogitf}} as defined by van Ewijk and Hoekstra 1993 is + fitted to the data. Default is FALSE. Obtaining the ED50 (and EDx values + in general) uses \code{\link{ED}} internally and does not always give a + result. + } + \item{level}{ + The level for the confidence interval listed for the log ED50.} + \item{chooseone}{ + If TRUE (default), the models are tried in the order linlogit, probit, + logit, weibull, and the first model that produces a valid fit is used. + If FALSE, all models that are set to TRUE and that can be fitted will be + reported.} + \item{EDx}{ + A vector of inhibition values x in percent for which the corresponding doses + EDx should be reported. + } + \item{showED50}{ + If set to TRUE, the ED50 and its confidence interval on the original dose + scale (not log scale) is included in the output. + } +} +\value{ + \item{results}{ + A data frame containing at least one line for each substance. 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. Every successful fit is + reported in one line. Parameters of the fitted curves are only reported + if the fitted ED50 is not higher than the highest dose. + + \code{ndl} is the number of dose levels in the raw data, \code{n} is the + total number of data points in the raw data used for the fit + \code{lld} is the decadic logarithm of the lowest dose and + \code{lhd} is the decadic logarithm of the highest dose. + + If the parameter \code{showED50} was set to TRUE, the ED50 values and their + confidence intervals are also included on the original dose scale. + + If one or more response leves were specified in the argument \code{EDx}, + the corresponding dose levels are given, together with their confidence + intervals. + } +} +\examples{ +data(antifoul) +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)}} +\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} + \url{http://www.uft.uni-bremen.de/chemie/ranke} +} +\keyword{models} +\keyword{regression} +\keyword{nonlinear} diff --git a/man/drfit.Rd b/man/drfit.Rd index 7237404..fe84a91 100644 --- a/man/drfit.Rd +++ b/man/drfit.Rd @@ -114,6 +114,9 @@ If the parameter \code{showED50} was set to TRUE, the ED50 values and their confidence intervals are also included on the original dose scale. + + If one or more response leves were specified in the argument \code{EDx}, + the corresponding dose levels are given in addition. } } \examples{ @@ -123,6 +126,11 @@ format(r, digits = 2) } \note{There is a demo for each dataset that can be accessed by \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} diff --git a/man/drplot.Rd b/man/drplot.Rd index b2c2745..e9e4dd1 100644 --- a/man/drplot.Rd +++ b/man/drplot.Rd @@ -8,7 +8,7 @@ \usage{ drplot(drresults, data, dtype, alpha, ctype, path, fileprefix, overlay, xlim, ylim, xlab, ylab, axes, frame.plot, postscript, - pdf, png, bw, pointsize, colors, ltys, devoff, lpos) + pdf, png, bw, pointsize, colors, ltys, pchs, devoff, lpos) } \arguments{ \item{drresults}{ @@ -99,6 +99,11 @@ \item{ltys}{ This is a vector of line types for the dose-response models, defaulting to 1:8. } + \item{pchs}{ + This is a vector of character types for the data. The default uses built-in + characters 1:n with n being the number of substances for which data are plotted + for overlays, or always 1 when no overlay plot is generated. + } \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 |