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CRAN: Package anovir

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>.

Documentation: Reference manual: anovir.html , anovir.pdf Vignettes: Introduction (source, R code)
Confidence intervals (source, R code)
Data format (source, R code)
Likelihood functions described (source, R code)
Modifying nll functions (source, R code)
Using nll functions (source, R code)
Probability distribution functions (source, R code)
Starting values (source, R code)
The exponential distribution (source, R code)
Worked examples I (source, R code)
Worked examples II (source, R code)
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