Package: anovir 0.1.0

anovir: Analysis of Virulence

Epidemiological population dynamics models traditionally define a pathogen's virulence as the increase in the per capita rate of mortality of infected hosts due to infection. This package provides functions allowing virulence to be estimated by maximum likelihood techniques. The approach is based on the analysis of relative survival comparing survival in matching cohorts of infected vs. uninfected hosts (Agnew 2019) <doi:10.1101/530709>.

Authors:Philip Agnew [aut, cre], Jimmy Lopez [aut]

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20 exports 0.00 score 7 dependencies 20 scripts 209 downloads

Last updated 4 years agofrom:80ffca0c6b. Checks:OK: 7. Indexed: yes.

Exports:av_long_infectedav_long_uninfectedcheck_dataconf_ints_virulenceetd_infectedetd_uninfectednll_basicnll_basic_logscalenll_controlsnll_exposed_infectednll_frailtynll_frailty_correlatednll_frailty_logscalenll_frailty_sharednll_proportional_virulencenll_recoverynll_recovery_IInll_two_inf_subpops_obsnll_two_inf_subpops_unobssim_data_nll_basic

Dependencies:bbmlebdsmatrixlatticeMASSMatrixmvtnormnumDeriv