HTdatasim: Simulates picking colonies data from a serial transfer...

In javirudolph/StabilityToolkit: Statistical inference for bacterial stability assays

Description

using the solution of the difference equation for the fraction of plasmid-free cells for the Horizontal Transfer model. Calls the HT.predict() function. See Ponciano et al 2007.

Usage

HTdatasim(beta.o, lam, sig, theta, gam, days, gen, Dmat)

Arguments

beta.o	Initial fraction of plasmid free cells
lam	Segregation rate (a number between 0 and 1)
sig	plasmid cost. Usually sig>0 but if -1<sig<0, then this parameter represents the benefit of having a plasmid
theta	fraction of plasmid free cells at which the horizontal transfer attains half its maximum
gam	Horizontal transfer probability
days	vector
gen	Number of generations per day
Dmat	A matrix whose number of rows is the number of days that the assay was ran. The number of columns corresponds to the number of replicated platings. The entries correspond to the total number of colonies picked for testing in a particular day and replicate.

Value

a vector of same length as 'says' with the fraction of plasmid free cells. The output is a matrix of the number of plasmid-free colonies picked over time. The number of columns of this matrix is equal to the number of specified replicates. The number of replicates is specified implicitly by the number of columns of Dmat.

javirudolph/StabilityToolkit documentation built on Jan. 3, 2021, 11:29 p.m.