\name{fitCellGrowths}
\alias{fitCellGrowths}
\title{Fit multiple growth curves}
\usage{
  fitCellGrowths(well, plot.folder = NULL,
    model = "locfit", xlab = "time",
    ylab = expression(log2(Absorption)), scaleX = 1,
    scaleY = log2, calibration = identity,
    fileParser = readYeastGrower,
    getWellIds = getWellIdsTecan, locfit.h = 3 * 60 * 60,
    bandwidths = seq(0.5 * 3600, 10 * 3600, length.out = 30),
    nFold = 10, nWell = 100, cutoff = 0.95, ...)
}
\arguments{
  \item{well}{data.frame with mandatory columns directory,
  filename, well. See \code{\link{wellDataFrame}}}

  \item{plot.folder}{see details}

  \item{model}{model to choose for fitting growth curve}

  \item{fileParser}{Converts the file generated by the
  machine to proper R format. See
  \code{\link{readYeastGrower}} for details.}

  \item{xlab}{plot parameter}

  \item{ylab}{plot parameter}

  \item{scaleX}{useful if you want to get the doubling in
  another unit, e.g. days instead of seconds.}

  \item{scaleY}{\code{function} applied to the calibrated
  data.}

  \item{calibration}{\code{function} or \code{list} of
  \code{functions}. If function, calibration is applied to
  all raw data. If list, the well dataframe must contain a
  column \code{machine}. Depending on that column the
  according function in the list is applied to the raw
  data. See details}

  \item{getWellIds}{function or vector. If function its
  parameter is the return value of fileParser. It should
  return a vector containing the well ids (e.g. A01, A02,
  ...). You can set the well ids vector directly. See
  \code{\link{getWellIdsTecan}}.}

  \item{locfit.h}{bandwidth parameter for local polynomial
  fitting. If set to "bandwidthCV" bandwidth is
  automatically selected through \code{\link{bandwidthCV}}}

  \item{bandwidths}{passed to \code{\link{bandwidthCV}} if
  locfit.h="bandwidthCV"}

  \item{nFold}{passed to \code{\link{bandwidthCV}} if
  locfit.h="bandwidthCV"}

  \item{nWell}{passed to \code{\link{bandwidthCV}} if
  locfit.h="bandwidthCV"}

  \item{cutoff}{passed to \code{\link{bandwidthCV}} if
  locfit.h="bandwidthCV"}

  \item{...}{Parameter is passed to
  \code{\link{fitCellGrowth}}}
}
\value{
  dataframe with entries \item{maxGrowthRate}{maximal
  growth rate} \item{pointOfMaxGrowthRate}{datapoint where
  growth rate is maximal} \item{max}{inferred maximum among
  the time points} \item{pointOfMax}{datapoint of the max
  fitted value}
}
\description{
  Fit growth curves for multiple wells
}
\details{
  Essentially a wrapper for \code{\link{fitCellGrowth}}.
  The function gets a well object and fits a growth curve
  on all wells. It computes the doubling frequency observed
  in a well and extracts the maximal growth rate (
  1/minimal doubling time). The raw values from the machine
  might not be directly optical densities (OD), which is
  needed to infer doubling time. Calibration functions for
  each machine can be provided to map raw values into OD
  using the \code{calibration} parameter. If the parameter
  plot.folder is set, the function creates a folder within
  plot.folder for each file in the well object. For each
  well a plot is written into that folder, named
  \code{well_id.png}.
}
\examples{
plateLayout <- system.file("extdata", "plateLayout.txt", package="cellGrowth")
machineRun <- system.file("extdata", "machineRun.txt", package="cellGrowth")
well <- wellDataFrame(plateLayout,machineRun)
cal <- function(x){x+1}
fit <- fitCellGrowths(well,plot.folder="data",calibration=cal)
}
\author{
  Julien Gagneur and Andreas Neudecker
}
\seealso{
  \code{\link{fitCellGrowth}}
}