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51 lines
2.3 KiB
51 lines
2.3 KiB
% Generated by roxygen2 (4.1.1): do not edit by hand
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% Please edit documentation in R/class.well.R
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\docType{class}
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\name{well-class}
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\alias{well-class}
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\title{Class that contains well data}
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\description{
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Class that contains well data
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}
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\section{Slots}{
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\describe{
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\item{\code{position}}{- 3-member vector containing identifying information for the well: row (letters), column (numbers) and plate ID.}
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\item{\code{well.info}}{- a list containing strain and media names if provided}
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\item{\code{screen.data}}{- a data frame with Time and raw OD values. This is the only slot that is filled upon creation of a well object.
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as different functions are run on the well the data frame gets filled with additional columns.}
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\item{\code{start.index}}{- integer index of the time point where growth curve starts, e.g. of the inoculation time point}
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\item{\code{use.log}}{- a single logical value denoting whether to return log-transformed values when data is requested from the well}
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\item{\code{norm}}{- a value to subtract from all OD values before returning data. filled by <normalize.ODs> (see normalize.and.transform.R)}
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\item{\code{curve.par}}{- a list of parameters that denote whether the well is empty, whether it contains ODs indicating a viable culture, whether it tanks at a certain timepoint.}
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\item{\code{fit.par}}{- will be a list containing the fitted model parameters}
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\item{\code{fit.std.err}}{- will be a list containing the standard errors for the fitted model parameters}
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\item{\code{equation}}{- will contain an expression for evaluating the successfully fitted model}
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\item{\code{model.name}}{- will contain the name of the successfully fit model}
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\item{\code{fit.info}}{- a message with info about whether the fit was successful, failed, or skipped.}
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\item{\code{add.info}}{- a message with info about whether jumps in OD were detected or removed, or if ODs were detected below the blank OD.}
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\item{\code{inflection.time}}{- the Time value at the point where the specific growth is located. no longer a formula param NWD}
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\item{\code{rss}}{- residual sum of squares}
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\item{\code{loess}}{- object returned by running loess on the normalized well data}
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\item{\code{nls}}{- object returned by running nls on the normalized well data}
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\item{\code{auc}}{- The area under the curve.}
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}}
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