The delta method | Setting confidence interval bounds | Worked example: 1 random variable | Worked example: 2 random variables | Part I: estimate parameter variables | Part II: calculate confidence intervals | Part III: compare results with those of conf_ints_virulence | Worked example: 3 random variables | Confidence intervals back-calculated from nll_basic_logscale | References

Introduction | General format required | Specific formats | nll_two_inf_subpops_obs | nll_recovery | nll_recovery_II

Population dynamics | Empirical setting | Survival functions | Relative survival | Relative survival and virulence | References

Introduction | Log-likelihood expressions: no censoring | Log-likelihood expressions: with censoring | Log-likelihood expressions: relative survival, with censoring | Likelihood functions in this package | The functions: | nll_basic | nll_basic_logscale | nll_controls | nll_exposed_infected | nll_frailty | nll_frailty_correlated | nll_frailty_logscale | nll_frailty_shared | nll_proportional_virulence | nll_recovery | nll_recovery_II | nll_two_inf_subpops_obs | nll_two_inf_subpops_unobs | Back to top | References

Introduction | Modifying nll_basic | Default: 4 variables to estimate | Modified: 5 variables to estimate | References

Parameters | Weibull distribution | Gumbel distribution | Fréchet distribution | Exponential distribution | back to top | Notes | Linear transformations of cumulative survival

Introduction | Linear regression of transformed cumulative survival data | Non-linear regression of cumulative survival data | Limitations to regression of cumulative survival data | Example | Linear regressions | Non-linear regressions | Maximum likelihood estimation | Compare models | References

Introduction | Example: background rate of mortality constant | References

Introduciton | Two-step preparation | Step #1 | Step #2 | References

Introduction | S06. Analysis of Blanford et al. data (i) | S08. Analysis of the Lorenz & Koella data | S10. Analysis of Blanford et al. data (ii) | S11. Analysis of Parker et al. data | S12. Exposed-but-uninfected hosts model | S14. Lorenz & Koella pooled data | S15. Shared and correlated frailty models | References

Extending nll_proportional_virulence to multiple treatments | Modifying nll_basic_logscale | References