MoWPP: Model of Within-host Pathogen Population dynamics

R code accompanying the manuscript entitled "Characterizing viral within-host diversity in fast and non-equilibrium demo-genetic dynamics" by Alamil M., Thébaud G., Berthier K. and Soubeyrand S.; v1.1 (August 10, 2022).

The code allows the user to run the model proposed by Alamil et al., which simulates within-host genetic diversity across time under various demo-genetic assumptions, at the nucleotide resolution (i.e., the diversity is represented in terms of genetic sequences). Several viral kinetics are implemented. Several options for defining the fitness of genotypes are available.

The code also allows the user to compute several diversity indices from the genetic sequences generated by the model, in particular the richness as well as the Shannon, Gini-Simpson and Jukes-Cantor diversity indices.