Analysis of Virulence

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Documentation for package ‘anovir’ version 0.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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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