diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/drfit.Rd | 84 | ||||
| -rw-r--r-- | man/drplot.Rd | 5 | ||||
| -rwxr-xr-x[-rw-r--r--] | man/linlogitf.Rd (renamed from man/linearlogisf.Rd) | 6 |
3 files changed, 60 insertions, 35 deletions
diff --git a/man/drfit.Rd b/man/drfit.Rd index 2ec4a73..0d9ee6f 100644 --- a/man/drfit.Rd +++ b/man/drfit.Rd @@ -6,58 +6,84 @@ biometric results for (eco)toxicity evaluation } \usage{ - drfit(data, startlogEC50 = NA, chooseone = TRUE, lognorm = TRUE, logis = FALSE, - linearlogis = FALSE, linearlogisWrong = NA, allWrong = NA, b0 = 2, f0 = 0) + drfit(data, startlogEC50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE, + weibull = FALSE, linlogit = FALSE, linlogitWrong = NA, allWrong = NA, + b0 = 2, f0 = 0) } \arguments{ \item{data}{ - A data frame as returned from \code{\link{drdata}}. The data frame has to + A data frame containing dose-response data. 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{\link{drplot}} function, a factor called "dosefactor" also has to be - present, containing the dose as a factor. If there is a column called "ok" - and it is set to "no fit", then the corresponding data point will be excluded - from the fitting procedure. + "dose" with the numeric dose values. 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 "ok" and it is set to "no fit" in a specific + line, then the corresponding data point will be excluded from the fitting + procedure, although it will be plotted. } \item{startlogEC50}{ - Especially for the linearlogis model, a suitable log10 of the EC50 has to be given + Especially for the linlogit 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.} - \item{lognorm}{ + \item{probit}{ A boolean defining if cumulative density curves of normal distributions - are fitted to the data. Default ist TRUE.} - \item{logis}{ - A boolean defining if cumulative densitiy curves of logistic distributions - are fitted to the data. Default is FALSE.} - \item{linearlogis}{ + \code{\link{pnorm}} are fitted against the decadic logarithm of the dose. + 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.} + \item{weibull}{ + A boolean defining if the cumulative density curves of weibull distributions + (\code{\link{pweibull}} with additionall location parameter and scale=1) + are fitted to the decadic logarithm of the dose. Default is FALSE.} + \item{linlogit}{ A boolean defining if the linear-logistic function - \code{\link{linearlogisf}} as defined by van Ewijk and Hoekstra 1993 is + \code{\link{linlogitf}} as defined by van Ewijk and Hoekstra 1993 is fitted to the data. Default is FALSE.} - \item{linearlogisWrong}{ + \item{linlogitWrong}{ An optional vector containing the names of the substances for which the - linearlogis function produces a wrong fit.} + linlogit function produces a wrong fit.} \item{allWrong}{ An optional vector containing the names of the substances for which all - functions produces a wrong fit.} + functions produce a wrong fit.} \item{chooseone}{ - If TRUE (default), the models are tried in the order linearlogis, logis and lognorm, - and the first model that produces a valid fit is used. Usually this will be the one - with the lowest residual standard deviation. If FALSE, all models that are set to TRUE - and that can be fitted will be reported.} + If TRUE (default), the models are tried in the order linlogit, weibull, + logit, probit, 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{b0,f0}{ If the linearlogistic model is fitted, b0 and f0 give the possibility to adapt the starting values for the parameters b and f.} } \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 "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.} - -} + 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 "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. + \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 + one of the model parameters that is being fitted, and therefore + a standard deviation \code{std} is reported for the logEC50. 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 + it is the standard deviation of the fitted normal distribution, in the case + of the "logit" fit it is the \code{scale} parameter in the \code{\link{plogis}} + function, and in the "weibull" fit it is the \code{shape} parameter of the + fitted \code{\link{pweibull}} function. Only the "linlogit" fit produces a + third parameter \code{c} which is the variable f from the + \code{\link{linlogitf}} function.} + } \examples{ data(antifoul) r <- drfit(antifoul) diff --git a/man/drplot.Rd b/man/drplot.Rd index ecd6895..e5201a2 100644 --- a/man/drplot.Rd +++ b/man/drplot.Rd @@ -80,9 +80,8 @@ } \note{ - Treatment of legends is not really well solved. Be sure all devices are - closed (e.g. by calling \code{dev.off()}) before calling \code{drplot} - again after a failure. + Be sure all devices are closed (e.g. by calling \code{dev.off()}) before + calling \code{drplot} again after a failure. } \examples{ data(antifoul) diff --git a/man/linearlogisf.Rd b/man/linlogitf.Rd index 1ebe8be..2eca8c4 100644..100755 --- a/man/linearlogisf.Rd +++ b/man/linlogitf.Rd @@ -1,12 +1,12 @@ -\name{linearlogisf} -\alias{linearlogisf} +\name{linlogitf} +\alias{linlogitf} \title{Linear-logistic function} \description{ Helper function describing a special type of dose-response curves, showing a stimulus at subtoxic doses. } \usage{ - linearlogisf(x,k,f,mu,b) + linlogitf(x,k,f,mu,b) } \arguments{ \item{x}{ |