fitRT-methods: Fitting Residence time (1-CDF)

Description Usage Arguments Details Value Examples

Description

Caclulate average residence time for trajecotries by fitting 1-CDF (survival distribution).

Usage

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fitRT(trackll=NULL,x.max=30,N.min=1.5,t.interval=0.5,maxiter.search=1e3,
maxiter.optim=1e3,k.ns=FALSE)

Arguments

t.interval

time interval for image aquisition. Default 0.5 sec.

maxiter.optim

A positive integer specifying the maximum number of iterations allowed for nls.

trackll

trajectory list generated by createTrackll() and processing. if NULL, user will be prompted to enter the trackll name.

x.max

The maximum range of X axis, i.e. time, for the output plot. Default 30 sec.

N.min

The minimal duration of trajectory length in the unit of s econd, trajectories shorter than N.min will be filtered out. Default 1.5 sec.

k.ns

Logical indicate or numeric used to control fitting.

maxiter.search

A positive integer specifying the maximum number of iterations allowed for nls.

Details

Calculating average residence time of particles by fitting 1-CDF (survival distribution) of its trajectorys.

Input track list (trackll) should be processed, merged trackll, the fitting will start right away after running the function. The maximum time range to be plotted can be set using x.max, this will not change the fitting result. The result of two-component fit will be shown on the plot as well as in the console. Fitting result is determined by the input trackll, and N.min (filtering of the trackll).

Value

Examples

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# Generate trackll, and process, 
# e.g. mask region of interest, merge tracks from multiple files.
folder=system.file("extdata","HSF",package="sojourner")
trackll=createTrackll(folder=folder, input=3)
trackll=maskTracks(folder,trackll)
trackll=mergeTracks(folder,trackll)

# Fit the residence time of trackll
fitRT(trackll=trackll,x.max=30,N.min=1.5,t.interval=0.5)

sheng-liu/sojourner documentation built on April 2, 2021, 2:30 a.m.