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 |