negloglikeSS: Computes the negative log-likelihood for the Segregation...

In javirudolph/StabilityToolkit: Statistical inference for bacterial stability assays

Description

Computes the negative log-likelihood for the Segregation Selection model, under binomial sampling See De Gelder et al 2004, 2008 and Ponciano et al 2007.

Usage

negloglikeSS(parm, day.counts, nreps, gen, D1)

Arguments

day.counts	is a matrix. The first column are the days, the next columns are the counts over time of the plasmid-free colonies. One column per replicated platings.
nreps	The number of replicated platings. Must be equal to ncol(day.counts)-1
gen	Number of generations per day
parm=c(beta.o, lam, sig)	which are the initial fraction of plasmid free cells, segregation rate and the plasmid cost. All three parameters must be specified according to the inverse transform of either the 1/(1+e-x) or the exp(x) functions. See example below
D1:	Either a matrix or a vector. If a matrix, its 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. If a vector, it is assumed that the daily number of colonies picked for each replicate is the same.

Value

the negative log-likelihood

Examples

negloglikeSS(parm, day.counts, nreps, gen,D1)

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