diff options
| -rw-r--r-- | man/IM1xIPC81.Rd | 20 | ||||
| -rw-r--r-- | man/IM1xVibrio.Rd | 21 | ||||
| -rw-r--r-- | man/checkexperiment.Rd | 6 | ||||
| -rw-r--r-- | man/drfit.Rd | 94 | ||||
| -rw-r--r-- | man/drplot.Rd | 19 | ||||
| -rw-r--r-- | man/pyrithione.Rd | 4 |
6 files changed, 82 insertions, 82 deletions
diff --git a/man/IM1xIPC81.Rd b/man/IM1xIPC81.Rd index 093f142..40aaa81 100644 --- a/man/IM1xIPC81.Rd +++ b/man/IM1xIPC81.Rd @@ -3,16 +3,16 @@ \alias{IM1xIPC81} \title{Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells} \description{ - This is the raw data documenting the influence of the alkyl - chain length in 3 position on the toxicity to the - promyelocytic leukemia rat cell line IPC-81. The substances - are named according to the UFT naming scheme of these - substances. IM13 BF4 means 1-methyl-3-propylimidazolium - tetrafluoroborate, IM14 BF4 means - 1-methyl-3-butylimidazolium tetrafluoroborate and IM1-10 - BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate. - This is a subset (only the BF4 anion) of the data - shown in Figure 3 in Ranke et al. (2004). + This is the raw data documenting the influence of the alkyl + chain length in 3 position on the toxicity to the + promyelocytic leukemia rat cell line IPC-81. The substances + are named according to the UFT naming scheme of these + substances. IM13 BF4 means 1-methyl-3-propylimidazolium + tetrafluoroborate, IM14 BF4 means + 1-methyl-3-butylimidazolium tetrafluoroborate and IM1-10 + BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate. + This is a subset (only the BF4 anion) of the data + shown in Figure 3 in Ranke et al. (2004). } \usage{data(IM1xIPC81)} \format{ diff --git a/man/IM1xVibrio.Rd b/man/IM1xVibrio.Rd index 79936d6..454e099 100644 --- a/man/IM1xVibrio.Rd +++ b/man/IM1xVibrio.Rd @@ -3,19 +3,20 @@ \alias{IM1xVibrio} \title{Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri} \description{ - This is the raw data documenting the influence of the alkyl chain length in 3 position - on the toxicity to the marine luminescent bacteria \emph{V. fischeri}. The substances - are named according to the UFT naming scheme of these substances. IM13 BF4 - means 1-methyl-3-propylimidazolium tetrafluoroborate, IM14 BF4 means - 1-methyl-3-butylimidazolium tetrafluoroborate and IM1-10 BF4 means - 1-methyl-3-decylimidazolium tetrafluoroborate. + This is the raw data documenting the influence of the alkyl chain length in 3 + position on the toxicity to the marine luminescent bacteria \emph{V. + fischeri}. The substances are named according to the UFT naming scheme of + these substances. + IM13 BF4 means 1-methyl-3-propylimidazolium tetrafluoroborate, + IM14 BF4 means 1-methyl-3-butylimidazolium tetrafluoroborate and + IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate. } \usage{data(IM1xVibrio)} \format{ - A dataframe containing the data as required for the \code{\link{drfit}} function. Additional - columns contain the species tested (luminescent bacteria Vibrio fischeri, \code{organism}), - and a field specifying if the data is regarded valid - (\code{ok}). + A dataframe containing the data as required for the \code{\link{drfit}} + function. Additional columns contain the species tested (luminescent bacteria + Vibrio fischeri, \code{organism}), and a field specifying if the data is + regarded valid (\code{ok}). } \source{ Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J, diff --git a/man/checkexperiment.Rd b/man/checkexperiment.Rd index 54352e8..d68cd87 100644 --- a/man/checkexperiment.Rd +++ b/man/checkexperiment.Rd @@ -14,9 +14,9 @@ \item{id}{ The id of the experiment or the plate identifying it within the database.} \item{db}{ - The database to be used. Currently, the microtiter plate databases - "cytotox", "enzymes" of the UFT Department of Bioorganic Chemistry are - supported, as well as the database of ecotoxicity experiments "ecotox".} + The database to be used. Currently, the microtiter plate databases + "cytotox", "enzymes" of the UFT Department of Bioorganic Chemistry are + supported, as well as the database of ecotoxicity experiments "ecotox".} } \value{ The function lists a report and shows two graphs side by side. diff --git a/man/drfit.Rd b/man/drfit.Rd index fefea85..9eb5476 100644 --- a/man/drfit.Rd +++ b/man/drfit.Rd @@ -2,31 +2,31 @@ \alias{drfit} \title{Fit dose-response models} \description{ - Fit dose-response relationships to dose-response data and calculate + Fit dose-response relationships to dose-response data and calculate biometric results for (eco)toxicity evaluation } \usage{ drfit(data, startlogED50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE, - weibull = FALSE, linlogit = FALSE, conf = FALSE, linlogitWrong = NA, - allWrong = NA, s0 = 0.5, b0 = 2, f0 = 0) + weibull = FALSE, linlogit = FALSE, conf = FALSE, linlogitWrong = NA, + allWrong = NA, s0 = 0.5, b0 = 2, f0 = 0) } \arguments{ \item{data}{ - A data frame containing dose-response data. The data frame has to contain - at least a factor called \dQuote{substance}, a numeric vector \dQuote{dose} - with the dose values, a vector called \dQuote{unit} containing the unit - used for the dose and a numeric vector \dQuote{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 \code{\link{drdata}}. - - If there is a column called \dQuote{ok} and it is set to \dQuote{no fit} in - a specific line, then the corresponding data point will be excluded from - the fitting procedure, although it will be plotted.} + A data frame containing dose-response data. The data frame has to contain + at least a factor called \dQuote{substance}, a numeric vector \dQuote{dose} + with the dose values, a vector called \dQuote{unit} containing the unit + used for the dose and a numeric vector \dQuote{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 \code{\link{drdata}}. + + If there is a column called \dQuote{ok} and it is set to \dQuote{no fit} in + a specific line, then the corresponding data point will be excluded from + the fitting procedure, although it will be plotted.} \item{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.} + 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.} \item{probit}{ A boolean defining if cumulative density curves of normal distributions \code{\link{pnorm}} are fitted against the decadic logarithm of the dose. @@ -44,9 +44,9 @@ \code{\link{linlogitf}} as defined by van Ewijk and Hoekstra 1993 is fitted to the data. Default is FALSE.} \item{conf}{ - A boolean defining if a confidence interval of the log ED50 is to be - listed for alpha = 5 \% (two-sided). If FALSE (default), the standard - deviation is listed in the output of drfit.} + A boolean defining if a confidence interval of the log ED50 is to be + listed for alpha = 5 \% (two-sided). If FALSE (default), the standard + deviation is listed in the output of drfit.} \item{linlogitWrong}{ An optional vector containing the names of the substances for which the linlogit function produces a wrong fit.} @@ -67,34 +67,34 @@ } \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 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. - \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, and - therefore, depending on the argument \code{conf}, a standard deviation - \code{std} or a confidence interval \code{conf} is reported for the - logED50. 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.} -} + \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, and + therefore, depending on the argument \code{conf}, a standard deviation + \code{std} or a confidence interval \code{conf} is reported for the + logED50. 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.} +} \examples{ data(antifoul) r <- drfit(antifoul) diff --git a/man/drplot.Rd b/man/drplot.Rd index 2f1d4ae..f8f8aa8 100644 --- a/man/drplot.Rd +++ b/man/drplot.Rd @@ -2,7 +2,7 @@ \alias{drplot} \title{Plot dose-response models} \description{ - Produce graphics of dose-response data and dose-response relationships + Produce graphics of dose-response data and dose-response relationships either combined or separately, for one or more substances. } \usage{ @@ -34,18 +34,18 @@ } \item{ctype}{ This argument decides if horizontal lines are drawn to show the scatter of - the control values (dose = 0), if there are more than three of them. - Defaults to "none", further allowed values are "std" and "conf" for - displaying the standard deviation of the controls or the confidence - interval for the mean of the controls. + the control values (dose = 0), if there are more than three of them. + Defaults to "none", further allowed values are "std" and "conf" for + displaying the standard deviation of the controls or the confidence + interval for the mean of the controls. } \item{path}{ The path where graphic files should be put if any are produced. Defaults to "./" i.e. the current working directory of R. } \item{fileprefix}{ - A string which will form the beginning of each filename, if graphic files - are created. Defaults to "drplot". + A string which will form the beginning of each filename, if graphic files + are created. Defaults to "drplot". } \item{overlay}{ If TRUE, all output will be put into one graph, otherwise a separate graph @@ -71,8 +71,8 @@ } \item{png}{ If TRUE, (a) png graph(s) will be created. Otherwise, and if the - postscript and pdf arguments are also FALSE, graphics will be displayed - with a screen graphics device. + postscript and pdf arguments are also FALSE, graphics will be displayed + with a screen graphics device. } \item{bw}{ A boolean deciding if the plots will be black and white or not. Default @@ -99,7 +99,6 @@ You will get plots of data and/or the fitted dose-response curves, on the screen and/or as postscript files, depending on the parameters. } - } \note{ Be sure all devices are closed (e.g. by calling \code{dev.off()}) before diff --git a/man/pyrithione.Rd b/man/pyrithione.Rd index 4ea72cc..b24a906 100644 --- a/man/pyrithione.Rd +++ b/man/pyrithione.Rd @@ -9,8 +9,8 @@ } \usage{data(pyrithione)} \format{ - A dataframe containing the data as required for the \code{\link{drfit}} function. -} + A dataframe containing the data as required for the \code{\link{drfit}} + function. } \source{ Doose C, Ranke J, Stock F, Bottin-Weber U, Jastorff B (2004) Structure-activity relationships of pyrithiones - IPC-81 toxicity tests with |