toggle_mutation_matrix: Toggles the mutation matrix to reflect mutation and...

In philliplab/hdsResistanceModel: Hybrid Dynamic/Stochastic Model of HIV Resistance Evolution

Description

It takes a full matrix and switches off specific strains

Usage

  toggle_mutation_matrix(E, strains, type, N_S)

Arguments

E	The mutation matrix
strains	The indices of the strains that must be switched off
type	The type of the matrix to return continuous or discrete
N_S	The number of strains in the matrix not strictly required - should this parameter be removed?

Details

The mutation matrix contains the probabilities that each strain will mutate into another strain in a single replication. The continuous version of the matrix is used in the equations for the dynamical part of the system. The discrete version of the matrix is used in the equation that computes the probability of a mutation not arising.

If a strain is extinct (or off) then it is not part of the dynamical system, so all elements in both the rows and columns of the extinct strains are set to zero.

If a strain is extinct, then it does not reproduce and as such does not produce mutations. Thus the elements in the columns of the extinct strains are set to zero. If a strain is not extinct, then the probability of it mutating from another strain is tracked in the dynamic portion of the equations and not in the stochastic portions of the equations. Thus all elements in the rows of strains that are NOT extinct is set to zero.

philliplab/hdsResistanceModel documentation built on May 25, 2019, 5:05 a.m.