fitNeutralDrift: Fit crypt neutral drift model.

In MorrisseyLab/CryptDriftR: Analyse crypt lineage tracing data

Description

fitNeutralDrift will run an mcmc algorithm to infer the parameters from the neutral drift model.

Usage

fitNeutralDrift(
  x,
  time_interval,
  max_iter = 40000,
  n_par_chains = 2,
  burn_in = 5000,
  thin = 20
)

Arguments

x	Clone size counts. With a column per day and a row per size clone size.
time_interval	vector of time point values. Should have same number of elements as columns in x.
max_iter	number of mcmc iterations to run.
n_par_chains	number of parallel chains (and cpus used) to run.
burn_in	mcmc burn in
thin	mcmc thining

Value

Will retrun a list that can be used directly with the plotting functions. The list contains an mcmc matrix, the data and time vector used to fit, as well as the MAP estimate of the parameters.

Examples

time_points = c(4, 7, 10, 14, 21)
x = simulateNeutralDriftData(0.1, 5, 2, time_points, 8, 300)
fit_out = fitNeutralDrift(x, time_points)
plotsConvergence_Neutral(fit_out)
plotsNeutralDrift_Fit(fit_out)

MorrisseyLab/CryptDriftR documentation built on Aug. 7, 2021, 8:22 p.m.