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>.

Version: 0.1.0
Depends: bbmle, R (≥ 2.10), stats4
Suggests: knitr, rmarkdown, stats, testthat
Published: 2020-10-24
Author: Philip Agnew [aut, cre], Jimmy Lopez [aut]
Maintainer: Philip Agnew <philip.agnew at ird.fr>
License: GPL-3
URL: https://www.biorxiv.org/content/10.1101/530709v1
NeedsCompilation: no
CRAN checks: anovir results

Downloads:

Reference manual: anovir.pdf
Vignettes: Introduction
Confidence intervals
Data format
Likelihood functions described
Modifying nll functions
Using nll functions
Probability distribution functions
Starting values
The exponential distribution
Worked examples I
Worked examples II
Package source: anovir_0.1.0.tar.gz
Windows binaries: r-devel: anovir_0.1.0.zip, r-release: anovir_0.1.0.zip, r-oldrel: anovir_0.1.0.zip
macOS binaries: r-release: anovir_0.1.0.tgz, r-oldrel: anovir_0.1.0.tgz

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