doublingTime: Calculate doubling times

In whitwort/plateKinetics: Analysis of kinetic reads from multiwell plates

Description

This function calculates doubling times for microbial cultures using time series data for each well in an experiment. By default this analysis proceedure picks optical density readings using lag and plateau phase filters and fits a log model.

Usage

doublingTime(experiment, value, mapName = paste(reduceName, "included", sep =
  "."), reduceName = "doublingTime", filters = c("Lag", "Plateau"),
  filterFuncs = lapply(filters, function(name) {     dt.filters[[name]]$func
  }), timeFormat = "none", formatFunc = dt.timeFormats[[timeFormat]]$func)

Arguments

experiment	An experiment object, usually created by loadExperiment.
value	The name of a value on experiment$map to use for optical density.
mapName	The name of the column on the $map data.frame to use to save information about which time points were included when calculating the doubling time.
reduceName	The name of the column on the $reduce data.frame to use to save the doubling time for each well.
filters	A character vector with the ids of filters to use. See dt.filters for available filters. Alternatively, use filterFuncs to pass in a list of functions directly.
filterFuncs	A list of OD filter functions. Each should take an od vector as the sole argument. Alternatively, specify filters.
timeFormat	A chacater vector naming the time formatter to use. See dt.timeFromats for available options. Alternatively use formatFunc to pass the function in directly.
formatFunc	A time formatter function.

Value

An updated experiment object with new/updated columns on $map and $reduce.

whitwort/plateKinetics documentation built on May 4, 2019, 5:23 a.m.