Description Usage Arguments Details Value Author(s) Examples
Perform crossvalidation to detect optimal bandwidth
1 2 3 4 5  bandwidthCV(well, fileParser = readYeastGrower,
getWellIds = getWellIdsTecan,
bandwidths = seq(0.5 * 3600, 10 * 3600, length.out = 30),
nFold = 10, nWell = 100, cutoff = 0.95,
calibration = identity, scaleY = log2)

well 
well dataframe. See

fileParser 
Converts the file generated by the
machine to proper R format. See

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

bandwidths 
vector of bandwidths to test on 
nFold 

nWell 

cutoff 

calibration 

scaleY 

This function needs a few minutes time. The "optimal"
bandwidth is the largest bandwidth which is in 95%
(cutoff parameter) of all cases within one standard
deviation of the best bandwidth. This should make the
derivative of the fitted curve more robust. 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 calibration
parameter.
list with entries
bandwidth 
"optimal" bandwidth 
well 
well dataframe 
bandwidths 
tested bandwidths 
err2 
squared error 
err2std 
Standard deviation of squared error 
muStd 
Standard deviation of max growth rate 
oneStdOfMini 
bandwidths within one std of best 
Julien Gagneur and Andreas Neudecker
1 2 3 4 5  folder < system.file("extdata", package="cellGrowth")
well < wellDataFrame(file.path(folder, "plateLayout.txt"), file.path(folder,"machineRun.txt"))
## for a fast example, we use nWell = 1 here. Use a large number (default 100) for real life applications
bw < bandwidthCV(well, nWell=1)

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