hivpopulation Overview

hivpopulation is a subclass of haploid_highd, hence inherits its methods. Moreover, hivpopulation has some HIV-specific methods.

hivpopulation has two phenotypic traits, replication and resistance. They contribute linearly to the viral fitness. The relative weight is set by the attribute treatment.

Note

Clicking on the name of the function will take you to a more detailed explanation listing all arguments.

Initialization

hivpopulation.__init__

Construct a HIV population with certain parameters.

Drug Treatment

hivpopulation.treatment

Treatment weight (between 0 and 1) ..

Replication and Resistance

hivpopulation.set_trait_landscape	Set HIV trait landscape according to some general parameters.
hivpopulation.set_replication_landscape	Set the phenotypic landscape for the replication capacity of HIV.
hivpopulation.set_resistance_landscape	Set the phenotypic landscape for the drug resistance of HIV.
hivpopulation.get_replication_additive	The additive part of the replication lansdscape.
hivpopulation.get_resistance_additive	The additive part of the resistance lansdscape.
hivpopulation.set_replication_additive	Set the additive replication coefficients
hivpopulation.set_resistance_additive	Set the additive drug resistance coefficients

I/O Convenience Functions

hivpopulation.read_replication_coefficients	Read replication coefficients from a text file
hivpopulation.read_resistance_coefficients	Read resistance coefficients from a text file
hivpopulation.write_genotypes	Store random genotypes into a plain text file.
hivpopulation.write_genotypes_compressed	Store random genotypes into a compressed file.