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anovir (version 0.1.0)

Analysis of Virulence

Description

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) .

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Version

Install

install.packages('anovir')

Monthly Downloads

215

Version

0.1.0

License

GPL-3

Maintainer

Philip Agnew

Last Published

October 24th, 2020

Functions in anovir (0.1.0)

data_blanford

Full data from Blanford et al (2012)
nll_recovery

Negative log-likelihood function: recovery model
nll_proportional_virulence

Negative log-likelihood function: nll proportional virulence
nll_frailty_logscale

Negative log-likelihood function: frailty variables on logscale
nll_frailty_shared

Negative log-likelihood function: frailty shared
nll_two_inf_subpops_unobs

Negative log-likelihood function: two unobserved subpopulations of infected hosts
recovery_data

Simulated recovery data
nll_frailty_correlated

Negative log-likelihood function: correlated frailty model
nll_frailty

Negative log-likelihood function: frailty
nll_recovery_II

Negative log-likelihood function: recovery model, no background mortality
nll_basic

Negative log-likelihood function: basic model
nll_basic_logscale

Negative log-likelihood function: basic model on logscale
nll_two_inf_subpops_obs

Negative log-likelihood function: two observed subpopulations of infected hosts
nll_exposed_infected

Negative log-likelihood function: exposed-infected
nll_controls

Negative log-likelihood function: control data only
recovery_data_II

Simulated recovery data, with no background mortality
sim_data_nll_basic

Function simulating survival data for nll_basic
conf_ints_virulence

Approximate 95% confidence intervals for virulence
etd_uninfected

Expected time of death: uninfected hosts
data_parker

Full data from Parker et al (2014)
data_lorenz

A subset of data from Lorenz & Koella (2011)
etd_infected

Expected time of death: infected hosts
av_long_uninfected

Average longevity: estimate for uninfected hosts
anovir-package

anovir: Analysis of Virulence
av_long_infected

Average longevity: estimate for infected hosts
check_data

Checks data are correctly described for models