Description Usage Arguments Value
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.
1 2 3 4 | 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)
|
experiment |
An experiment object, usually created by
|
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
|
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
|
formatFunc |
A time formatter function. |
An updated experiment object with new/updated columns on $map and $reduce.
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