plot_MSD {AIUQ}R Documentation

Plot estimated MSD with uncertainty from SAM class

Description

Function to plot estimated MSD with uncertainty from SAM class, versus true mean squared displacement(MSD) or given reference values.

Usage

plot_MSD(object, msd_truth = NA, title = NA, log10 = TRUE)

Arguments

object

an S4 object of class SAM

msd_truth

a vector/matrix of true MSD or reference MSD value, default is NA

title

main title of the plot. If NA, title is "model_name" with model_name being a field in SAM class representing fitted model.

log10

a logical evaluating to TRUE or FALSE indicating whether a plot in log10 scale is generated

Value

A plot of estimated MSD with uncertainty versus truth/reference values.

Author(s)

Yue He [aut], Xubo Liu [aut], Mengyang Gu [aut, cre]

References

Gu, M., He, Y., Liu, X., & Luo, Y. (2023). Ab initio uncertainty quantification in scattering analysis of microscopy. arXiv preprint arXiv:2309.02468.

Gu, M., Luo, Y., He, Y., Helgeson, M. E., & Valentine, M. T. (2021). Uncertainty quantification and estimation in differential dynamic microscopy. Physical Review E, 104(3), 034610.

Examples

library(AIUQ)

## Simulate BM and get estimated parameters with uncertainty using BM model
# Simulation
set.seed(1)
sim_bm = simulation(sz=100,len_t=100,sigma_bm=0.5)
show(sim_bm)

# AIUQ method: fitting using BM model
sam = SAM(sim_object=sim_bm, uncertainty=TRUE,AIUQ_thr=c(0.999,0))
show(sam)

plot_MSD(object=sam, msd_truth=sam@msd_truth) #in log10 scale
plot_MSD(object=sam, msd_truth=sam@msd_truth,log10=FALSE) #in real scale


[Package AIUQ version 0.5.1 Index]