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authorranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>2014-02-25 21:26:05 +0000
committerranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>2014-02-25 21:26:05 +0000
commit189aad5e39df513075fc7c7a64e646b1a354bc4c (patch)
tree39d44b4495eab9893e4c90eaefb78d4ff96ea6b5
parent35362cfc7c02f12fd9689f68a772a804d895535a (diff)
More detailed documentation of the result dataframe returned
by drfit and drcfit. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@99 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
-rw-r--r--man/drcfit.Rd95
-rw-r--r--man/drfit.Rd111
2 files changed, 148 insertions, 58 deletions
diff --git a/man/drcfit.Rd b/man/drcfit.Rd
index 2da0418..b10418a 100644
--- a/man/drcfit.Rd
+++ b/man/drcfit.Rd
@@ -25,11 +25,10 @@
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.
+ 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.}
+ as a here, and parameter b from there 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.
@@ -66,27 +65,74 @@
}
}
\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.
+ A dataframe with the attribute \code{models} holding a list of the fitted
+ dose-response models of class \code{\link{nls}}. The dataframe has at least
+ one line for each substance.
- \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.
+ The following variables are in the dataframe:
+ \item{Substance}{
+ The name of the substance
+ }
+ \item{ndl}{
+ The number of dose levels in the raw data
+ }
+ \item{n}{
+ The total number of data points in the raw data used for the fit
+ }
+ \item{lld}{
+ The decadic logarithm of the lowest dose
+ }
+ \item{lhd}{
+ The total number of data points in the raw data used for the fit
+ }
+ \item{mtype}{
+ 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. If the fitted ED50
+ is higher than the highest dose, \dQuote{no fit} is given here.
+ }
+ \item{logED50}{
+ The decadic logarithm of the ED50
+ }
+ \item{low \%}{
+ The lower bound of the confidence interval of log ED50.
+ The name of the column depends on the requested confidence \code{level}.
}
+ \item{high \%}{
+ The higher bound of the confidence interval of log ED50.
+ The name of the column depends on the requested confidence \code{level}.
+ }
+ \item{unit}{
+ The unit used for the dose levels in the dose-response data
+ }
+ \item{sigma}{
+ The square root of the estimated variance of the random error as returned
+ by \code{\link{summary.drc}}.
+ }
+ \item{a}{
+ For the linlogit model, this is the parameter e from \code{\link{BC.4}}.
+ For the probit and the logit model, this is the ED50. For the weibull
+ model, this is parameter e from \code{\link{W1.2}}. Note that the Weibull
+ model is fitted to the untransformed data.
+ }
+ \item{b}{
+ For the linlogit, probit, logit and weibull models, these are the
+ parameters b from \code{\link{BC.4}}, \code{\link{LN.2}},
+ \code{\link{LL.2}} and \code{\link{W1.2}}, respectively.
+ Note that the parameter definitions (and in the case of Weibull, the model
+ used) are different to the ones used in \code{\link{drfit}}.
+ }
+ \item{c}{
+ Only the \dQuote{linlogit} fit produces a third parameter \code{c}, which is
+ the parameter f from the \code{\link{BC.4}} function.
+ }
+ 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, together with their
+ confidence intervals as calculated by \code{\link{ED}} from the drc package.
}
\examples{
data(antifoul)
@@ -101,9 +147,10 @@ format(r, digits = 2)
\code{\link{IM1xVibrio}}.
}
\author{
- Johannes Ranke
- \email{jranke@uni-bremen.de}
+ Johannes Ranke \email{jranke@uni-bremen.de}
\url{http://www.uft.uni-bremen.de/chemie/ranke}
+ The functionality of the drc package used under the hood in this function
+ was written by Christian Ritz.
}
\keyword{models}
\keyword{regression}
diff --git a/man/drfit.Rd b/man/drfit.Rd
index fe84a91..3729550 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -40,7 +40,9 @@
\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.}
+ are fitted to the decadic logarithm of the dose. Default is FALSE.
+ Note that the weibull distribution is fitted here to the log transformed doses
+ which appears to be an uncommon approach.}
\item{linlogit}{
A boolean defining if the linear-logistic function
\code{\link{linlogitf}} as defined by van Ewijk and Hoekstra 1993 is
@@ -83,41 +85,79 @@
}
}
\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.
+ A dataframe with the attribute \code{models} holding a list of the fitted
+ dose-response models of class \code{\link{nls}}. The dataframe has at least
+ one line for each substance.
- \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. For the
- \dQuote{linlogit}, \dQuote{logit} and \dQuote{probit} models, the
- parameter \code{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 \code{level} is calculated
- using the \code{\link[MASS:confint]{confint.nls}} function and listed.
- In the case of the \dQuote{weibull} model, \code{a} is a
- location parameter. Parameter \code{b} in the case of the
- \dQuote{linlogit} fit is the variable b from the \code{\link{linlogitf}}
- function. In the case of \dQuote{probit} fit it is the standard deviation
- of the fitted normal distribution, in the case of the \dQuote{logit} fit
- it is the \code{scale} parameter in the \code{\link{plogis}} function,
- and in the \dQuote{weibull} fit it is the \code{shape} parameter of the
- fitted \code{\link{pweibull}} function. Only the \dQuote{linlogit} fit
- produces a third parameter \code{c} which is the variable f from the
- \code{\link{linlogitf}} function.
-
- 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.
+ For the \dQuote{linlogit}, \dQuote{logit} and \dQuote{probit} models, the
+ parameter \code{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 \code{level} is calculated
+ using the \code{\link[MASS:confint]{confint.nls}} function and listed.
+
+ The following variables are in the dataframe:
+ \item{Substance}{
+ The name of the substance
+ }
+ \item{ndl}{
+ The number of dose levels in the raw data
+ }
+ \item{n}{
+ The total number of data points in the raw data used for the fit
+ }
+ \item{lld}{
+ The decadic logarithm of the lowest dose
+ }
+ \item{lhd}{
+ The total number of data points in the raw data used for the fit
+ }
+ \item{mtype}{
+ 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. If the fitted ED50
+ is higher than the highest dose, \dQuote{no fit} is given here.
+ }
+ \item{logED50}{
+ The decadic logarithm of the ED50
+ }
+ \item{low \%}{
+ The lower bound of the confidence interval of log ED50.
+ The name of the column depends on the requested confidence \code{level}.
}
+ \item{high \%}{
+ The higher bound of the confidence interval of log ED50.
+ The name of the column depends on the requested confidence \code{level}.
+ }
+ \item{unit}{
+ The unit used for the dose levels in the dose-response data
+ }
+ \item{sigma}{
+ The square root of the estimated variance of the random error as returned
+ by \code{\link{summary.nls}}.
+ }
+ \item{a}{
+ For the \dQuote{linlogit}, \dQuote{logit} and \dQuote{probit} models, the
+ parameter \code{a} coincides with the logED50. In the case of the
+ \dQuote{weibull} model, \code{a} is a location parameter.
+ }
+ \item{b}{
+ Parameter \code{b} in the case of the \dQuote{linlogit} fit is the variable
+ b from the \code{\link{linlogitf}} function. In the case of \dQuote{probit}
+ fit it is the standard deviation of the fitted normal distribution, in the
+ case of the \dQuote{logit} fit it is the \code{scale} parameter in the
+ \code{\link{plogis}} function, and in the \dQuote{weibull} fit it is the
+ \code{shape} parameter of the fitted \code{\link{pweibull}} function.
+ }
+ \item{c}{
+ Only the \dQuote{linlogit} fit produces a third parameter \code{c} which is
+ the variable f from the \code{\link{linlogitf}} function.
+ }
+ 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{
data(antifoul)
@@ -130,6 +170,9 @@ format(r, digits = 2)
Further examples are given in help pages to the datasets
\code{\link{antifoul}}, \code{\link{IM1xIPC81}} and
\code{\link{IM1xVibrio}}.
+ Since version 0.6.1 of this package, there is a drop-in replacement function
+ \code{\link{drcfit}} which internally uses the drc package and also gives
+ confidence intervals for EDx values via this package.
}
\author{
Johannes Ranke

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