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

In javirudolph/StabilityToolkit: Statistical inference for bacterial stability assays

Description

Simulates picking colonies data from a serial transfer experiment using the solution of the difference equation for the fraction of plasmid-free cells for the Segregation Selection model. Calls the SS.predict() function. See De Gelder et al 2004, 2008 and Ponciano et al 2007.

Usage

SSdatasim(beta.o, lam, sig, 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
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.

Examples

mydmat <- matrix(52,nrow=8,ncol=3)
mydays <- 0:(nrow(mydmat)-1)
SSdatasim(beta.o=0.01, lam=0.003,sig=0.4, days=7, gen=mydays, Dmat=mydmat)

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