drfit                 package:drfit                 R Documentation

_F_i_t _d_o_s_e-_r_e_s_p_o_n_s_e _m_o_d_e_l_s

_D_e_s_c_r_i_p_t_i_o_n:

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

_U_s_a_g_e:

       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)

_A_r_g_u_m_e_n_t_s:

    data: A data frame containing dose-response data. The data frame
          has to contain at least a factor called "substance", a
          numeric vector "dose" with the dose values, a vector called
          "unit" containing the unit used for the dose and a numeric
          vector "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 '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.

startlogED50: Especially for the linlogit model, a suitable log10 of
          the ED50 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.

   level: The level for the confidence interval listed for the log
          ED50.

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.

     ps0: If the probit model is fitted, 'ps0' gives the possibility to
          adjust the starting value for the scale parameter of 'pnorm'.

     ls0: If the logit model is fitted, 'ls0' gives the possibility to
          adjust the starting value for the scale parameter of
          'plogis'.

     ws0: If the weibull model is fitted, 'ws0' 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.

_V_a_l_u_e:

 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 "inactive". If the mean
          response at the lowest dose is smaller than 0.5, the
          modeltype is set to "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. 

          'ndl' is the number of dose levels in the raw data, 'n' is
          the total number of data points in the raw data used for the
          fit '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 logED50, i.e the logED50
          is one of the model parameters that is being fitted.
          Therefore, a confidence interval for the confidence level
          'level' is calculated using the 'confint.nls' function and
          listed. 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.

_N_o_t_e:

     There is a demo for each dataset that can be accessed by
     'demo(dataset)'

_A_u_t_h_o_r(_s):

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

_E_x_a_m_p_l_e_s:

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

