javirudolph/StabilityToolkit: Statistical inference for bacterial stability assays

This package contains functions to estimate plasmid cost, segregation rate and horizontal transfer rates from stability assays data. The stability asays follow periodically (usually every 24 hours) the changes in the fraction of plasmid free cells in serial passage cultures. At the end of each cycle, the experimenter takes a sample of the liquid culture and plates it after dilution. Using an antibiotic marker present in the plasmid, the experimenter can count, out of a total number of colonies plated, how many of these are plasmid-carrying. Here, we provide an array of statistical and mathematical functions to estimate the parameters of a series of dynamic models consisting of a pair of difference equations that follow the abundance of plasmid-free and plasmid-carrying cells under various biological hypotheses. The package also includes functions to simulate data under each model. Estimation is done via Maximum Likelihood. Hierarchical stochastic models are also considered. Further information can be found in the author papers made in collaboration with Eva Top, see: http://people.clas.ufl.edu/josemi/papers/

install.packages("remotes")
remotes::install_github("javirudolph/StabilityToolkit")