Package: anovir 0.1.0

anovir: Analysis of Virulence

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) <doi:10.1101/530709>.

Authors:Philip Agnew [aut, cre], Jimmy Lopez [aut]

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anovir.pdf |anovir.html✨
anovir/json (API)

# Install 'anovir' in R:
install.packages('anovir', repos = c('https://philipagnew.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.34 score 20 scripts 211 downloads 20 exports 7 dependencies

Last updated from:80ffca0c6b. Checks:8 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK160
source / vignettesOK203
linux-release-x86_64OK157
macos-devel-arm64OK176
macos-release-arm64OK180
windows-develOK113
windows-releaseOK113
wasm-releaseOK96

Exports:av_long_infectedav_long_uninfectedcheck_dataconf_ints_virulenceetd_infectedetd_uninfectednll_basicnll_basic_logscalenll_controlsnll_exposed_infectednll_frailtynll_frailty_correlatednll_frailty_logscalenll_frailty_sharednll_proportional_virulencenll_recoverynll_recovery_IInll_two_inf_subpops_obsnll_two_inf_subpops_unobssim_data_nll_basic

Dependencies:bbmlebdsmatrixlatticeMASSMatrixmvtnormnumDeriv

Confidence intervals

Rendered fromconfidence_intervals.Rmdusingknitr::rmarkdownon Mar 22 2026.

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Data format

Rendered fromdata_format.Rmdusingknitr::rmarkdownon Mar 22 2026.

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Introduction

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Mar 22 2026.

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Likelihood functions described

Rendered fromnll_functions.Rmdusingknitr::rmarkdownon Mar 22 2026.

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Modifying nll functions

Rendered fromnll_functions_modifying.Rmdusingknitr::rmarkdownon Mar 22 2026.

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Probability distribution functions

Rendered fromprobability_distributions.Rmdusingknitr::rmarkdownon Mar 22 2026.

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Starting values

Rendered fromstarting_values.Rmdusingknitr::rmarkdownon Mar 22 2026.

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The exponential distribution

Rendered fromthe_exponential_distribution.Rmdusingknitr::rmarkdownon Mar 22 2026.

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Using nll functions

Rendered fromnll_functions_using.Rmdusingknitr::rmarkdownon Mar 22 2026.

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Worked examples I

Rendered fromworked_examples_I.Rmdusingknitr::rmarkdownon Mar 22 2026.

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Worked examples II

Rendered fromworked_examples_II.Rmdusingknitr::rmarkdownon Mar 22 2026.

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Readme and manuals

Help Manual

Help pageTopics
anovir: Analysis of Virulenceanovir-package anovir
Average longevity: estimate for infected hostsav_long_infected
Average longevity: estimate for uninfected hostsav_long_uninfected
Checks data are correctly described for modelscheck_data
Approximate 95% confidence intervals for virulenceconf_ints_virulence
Full data from Blanford et al (2012)data_blanford
A subset of data from Lorenz & Koella (2011)data_lorenz
Full data from Parker et al (2014)data_parker
Expected time of death: infected hostsetd_infected
Expected time of death: uninfected hostsetd_uninfected
Negative log-likelihood function: basic modelnll_basic
Negative log-likelihood function: basic model on logscalenll_basic_logscale
Negative log-likelihood function: control data onlynll_controls
Negative log-likelihood function: exposed-infectednll_exposed_infected
Negative log-likelihood function: frailtynll_frailty
Negative log-likelihood function: correlated frailty modelnll_frailty_correlated
Negative log-likelihood function: frailty variables on logscalenll_frailty_logscale
Negative log-likelihood function: frailty sharednll_frailty_shared
Negative log-likelihood function: nll proportional virulencenll_proportional_virulence
Negative log-likelihood function: recovery modelnll_recovery
Negative log-likelihood function: recovery model, no background mortalitynll_recovery_II
Negative log-likelihood function: two observed subpopulations of infected hostsnll_two_inf_subpops_obs
Negative log-likelihood function: two unobserved subpopulations of infected hostsnll_two_inf_subpops_unobs
Simulated recovery datarecovery_data
Simulated recovery data, with no background mortalityrecovery_data_II
Function simulating survival data for nll_basicsim_data_nll_basic