generateRateTransTemplate: Generate a state transition template matrix based on numbers...

In venelin/toyepidemic: Simulating epidemics with within-host strain mutation and between-host SIR dynamics

Description

Generate a state transition template matrix based on numbers of alleles at QTLs.

Usage

generateRateTransTemplate(numsAllelesAtSites, nameRows = FALSE)

Arguments

numsAllelesAtSites	integer vector specifying the number of alleles at each site, the length of the vector defining the number of QTLs.
nameRows	logical indicating whether the returned matrix should have named rows (for explicative purpose only, default FALSE). The column names are different for each row, i.e. the row-names excluding the genotype corresponding to that specific row.

Details

each element of the matrix is a multiplier for the corresponding genotype transition rate (see function simulateEpidemic in the patherit package). This multiplier is nonzero only for transitions that need exactly one mutation (haming distance = 1) in order to convert one genotype into another. The

venelin/toyepidemic documentation built on May 29, 2019, 11:46 a.m.