R: Analysis of Virulence

# Analysis of Virulence

## Documentation for package ‘anovir’ version 0.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

anovir-package | anovir: Analysis of Virulence
anovir | anovir: Analysis of Virulence
av_long_infected | Average longevity: estimate for infected hosts
av_long_uninfected | Average longevity: estimate for uninfected hosts
check_data | Checks data are correctly described for models
conf_ints_virulence | Approximate 95% confidence intervals for virulence
data_blanford | Full data from Blanford et al (2012)
data_lorenz | A subset of data from Lorenz & Koella (2011)
data_parker | Full data from Parker et al (2014)
etd_infected | Expected time of death: infected hosts
etd_uninfected | Expected time of death: uninfected hosts
nll_basic | Negative log-likelihood function: basic model
nll_basic_logscale | Negative log-likelihood function: basic model on logscale
nll_controls | Negative log-likelihood function: control data only
nll_exposed_infected | Negative log-likelihood function: exposed-infected
nll_frailty | Negative log-likelihood function: frailty
nll_frailty_correlated | Negative log-likelihood function: correlated frailty model
nll_frailty_logscale | Negative log-likelihood function: frailty variables on logscale
nll_frailty_shared | Negative log-likelihood function: frailty shared
nll_proportional_virulence | Negative log-likelihood function: nll proportional virulence
nll_recovery | Negative log-likelihood function: recovery model
nll_recovery_II | Negative log-likelihood function: recovery model, no background mortality
nll_two_inf_subpops_obs | Negative log-likelihood function: two observed subpopulations of infected hosts
nll_two_inf_subpops_unobs | Negative log-likelihood function: two unobserved subpopulations of infected hosts
recovery_data | Simulated recovery data
recovery_data_II | Simulated recovery data, with no background mortality
sim_data_nll_basic | Function simulating survival data for nll_basic