fitCDF-methods: fitCDF

In sheng-liu/smt: Single Molecule Tracking

Description

Caclulate apparent diffusion coefficient (Dcoef) for trajecotries by fitting displacementCDF.

Usage

fitCDF((cdf, components=c("one","two","three"),
        start=list(
            oneCompFit=list(D=c(1e-3,2)),
            twoCompFit=list(D1=c(1e-3,2),D2=c(1e-3,2),alpha=c(1e-3,1)),
            threeCompFit=list(D1=c(1e-3,2),D2=c(1e-3,2),D3=c(1e-3,2),
                              alpha=c(1e-3,1),beta=c(1e-3,1))),
        t.interval=0.01,
        maxiter.search=1e3,
        maxiter.optim=1e3,
        output=F,
        seed=NULL)

Arguments

start	the start value for fitting.
t.interval	time interval for image aquisition. Default 0.01 sec.
maxiter.optim	maximum iteration in local optimization process. Default ot 1000.
cdf	cdf calculated from displacementCDF().
components	parameter specifying the number of components to fit.Currently support one to three components fit.
maxiter.search	maximum iteration in random search start value process. defual to 1000.
output	Logical indicaring if output file should be generated.
seed	Seed for random number generator. This makes each run easily repeatable. Seed will be automatically assigned if no seed is specified (default). The seed information is stored as an attribute of the returned object. The seed can also be output to a txt file when output=T.

Details

calculating Dceof by fitting displacementCDF.

Reducing the range can greatly increase the precision of the searching; alternatively, if the range are unavailable, increase the maxiter.search so more points will be searched through with the cost of computation time. maxiter.optim barely need to change, if it does not converge with default setting maxiter=1e3, most likely the problem is in the initial values.

Value

• on screen output and file Result and parameters of goodness of the fit.

• Plot, fiting plot.

Examples

# compare folders
folder1=system.file("extdata","SWR1",package="smt")
folder2=system.file("extdata","HTZ1",package="smt")
trackll=compareFolder(c(folder1,folder2))
cdf=displacementCDF(trackll,dt=1,plot=F,output=F)

# specify ranges of parameter value of interest
fitCDF(cdf,components="two",
      start=list(
                twoCompFit=list(D1=c(1e-3,2),D2=c(1e-3,2),alpha=c(1e-3,1)))
                )

# repeat a fit
a=fitCDF(cdf,components="two",output=F)
b=fitCDF(cdf,components="two",output=F,seed=attr(a,"seed"))

# if result are identical
x=summary(a[[1]])
y=summary(b[[1]])
# formula records environment, exclude from the comparison
mapply(identical,x[names(x)!="formula"],y[names(y)!="formula"])

sheng-liu/smt documentation built on May 29, 2019, 9:22 p.m.