Description Usage Arguments Value Note Author(s) See Also Examples
Fit doseresponse relationships to doseresponse data and calculate biometric results for (eco)toxicity evaluation using the drc package
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data 
A data frame containing doseresponse 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 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. 
probit 
A boolean defining if cumulative density curves of normal distributions
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 
logit 
A boolean defining if cumulative density curves of logistic distributions

weibull 
A boolean defining if Weibull doseresponse models
( 
linlogit 
A boolean defining if the linearlogistic function

level 
The level for the confidence interval listed for the log ED50. 
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. 
EDx 
A vector of inhibition values x in percent for which the corresponding doses EDx should be reported. 
showED50 
If set to TRUE, the ED50 and its confidence interval on the original dose scale (not log scale) is included in the output. 
A dataframe with the attribute models
holding a list of the fitted
doseresponse models of class nls
. The dataframe has at least
one line for each substance.
The following variables are in the dataframe:
Substance 
The name of the substance 
ndl 
The number of dose levels in the raw data 
n 
The total number of data points in the raw data used for the fit 
lld 
The decadic logarithm of the lowest dose 
lhd 
The total number of data points in the raw data used for the fit 
mtype 
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. If the fitted ED50 is higher than the highest dose, “no fit” is given here. 
logED50 
The decadic logarithm of the ED50 
low % 
The lower bound of the confidence interval of log ED50.
The name of the column depends on the requested confidence 
high % 
The higher bound of the confidence interval of log ED50.
The name of the column depends on the requested confidence 
unit 
The unit used for the dose levels in the doseresponse data 
sigma 
The square root of the estimated variance of the random error as returned
by 
a 
For the linlogit model, this is the parameter e from 
b 
For the linlogit, probit, logit and weibull models, these are the
parameters b from 
c 
Only the “linlogit” fit produces a third parameter 
If the parameter 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 EDx
,
the corresponding dose levels are given in addition, together with their
confidence intervals as calculated by ED
from the drc package.
There is a demo for each dataset that can be accessed by
demo(dataset)
Johannes Ranke jranke@unibremen.de The functionality of the drc package used under the hood in this function was written by Christian Ritz.
Further examples are given in help pages to the datasets
antifoul
, IM1xIPC81
and
IM1xVibrio
.
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TBT: Fitting data...
Zn Pyrithion: Fitting data...
Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma a
1 TBT 38 135 2.7 2.4 probit 0.16 0.28 0.072 microM 0.19 0.68
2 Zn Pyrithion 27 81 2.1 2.0 probit 0.40 0.52 0.303 microM 0.23 0.40
b ED50 ED50 2.5% ED50 97.5% EDx5 EDx5 2.5% EDx5 97.5% EDx10 EDx10 2.5%
1 0.64 0.68 0.52 0.85 0.053 0.015 0.091 0.093 0.040
2 1.04 0.40 0.30 0.50 0.082 0.023 0.142 0.117 0.048
EDx10 97.5% EDx20 EDx20 2.5% EDx20 97.5%
1 0.15 0.18 0.11 0.26
2 0.19 0.18 0.10 0.26
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