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 |
msd_truth |
a vector/matrix of true MSD or reference MSD value,
default is |
title |
main title of the plot. If |
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