drfit {drfit}R Documentation

Fit dose-response models

Description

Fit dose-response relationships to dose-response data and calculate biometric results for (eco)toxicity evaluation

Usage

  drfit(data, startlogEC50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE,
    weibull = FALSE, linlogit = FALSE, linlogitWrong = NA, allWrong = NA, 
    s0 = 0.5, b0 = 2, f0 = 0)

Arguments

data 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. Such a data frame can be easily obtained if a compliant RODBC data source is available for use in conjunction with the function 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.
startlogEC50 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.
probit A boolean defining if cumulative density curves of normal distributions pnorm are fitted against the decadic logarithm of the dose. Default ist TRUE.
logit A boolean defining if cumulative density curves of logistic distributions plogis are fitted to the decadic logarithm of the dose. Default is FALSE.
weibull A boolean defining if the cumulative density curves of weibull distributions (pweibull with additionall location parameter and scale=1) are fitted to the decadic logarithm of the dose. Default is FALSE.
linlogit A boolean defining if the linear-logistic function linlogitf as defined by van Ewijk and Hoekstra 1993 is fitted to the data. Default is FALSE.
linlogitWrong An optional vector containing the names of the substances for which the linlogit function produces a wrong fit.
allWrong An optional vector containing the names of the substances for which all functions produce a wrong fit.
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.
s0 If the weibull model is fitted, s0 gives the possibility to adjust the starting value for the shape parameter of pweibull.
b0,f0 If the linearlogistic model is fitted, b0 and f0 give the possibility to adjust the starting values for the parameters b and f.

Value

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. n is the number of dose-response curves in the raw data (repetitions in each point), lld is the decadic logarithm of the lowest dose and lhd is the decadic logarithm of the highest dose. For the "linlogit", "logit" and "probit" models, the parameter 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 std is reported for the logEC50. In the case of the "weibull" model, a is a location parameter. Parameter b in the case of the "linlogit" fit is the variable b from the 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 scale parameter in the plogis function, and in the "weibull" fit it is the shape parameter of the fitted pweibull function. Only the "linlogit" fit produces a third parameter c which is the variable f from the linlogitf function.

Author(s)

Johannes Ranke jranke@uni-bremen.de http://www.uft.uni-bremen.de/chemie/ranke

Examples

data(antifoul)
r <- drfit(antifoul)
format(r,digits=2)

[Package drfit version 0.04-34 Index]