Add num_init_infect to probability_emergence()
#133
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This PR enhances the
probability_emergence()function by adding thenum_init_infectargument. This follows theprobability_epidemic(),probability_extinct()andprobability_contain()functions that have thenum_init_infectargument. This is an extension of the Antia et al. (2003) method which only included a single introduction.An illustration of the influence of multiple initial pathogen introductions on the probability of emergence is added to the
emergence.Rmdvignette.Multiple introductions is added to the unit test that checks for the equivalence between
probability_emergence()andprobability_epidemic().The default value for the
mutation_rateargument inprobability_emergence()is removed as this should always be specified by the user.