The Probability of Transmission Given Phylogenetic Linkage

Implements novel tools that estimate the probability of true transmission between two cases given phylogenetic linkage and the expected number of true transmission links in a sample. Methods described in Wohl, Giles, and Lessler (2021) .


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Reference manual

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install.packages("phylosamp")

0.1.6 by Justin Lessler, 13 days ago


https://github.com/HopkinsIDD/phylosamp


Report a bug at https://github.com/HopkinsIDD/phylosamp/issues


Browse source code at https://github.com/cran/phylosamp


Authors: John R Giles [aut, ctb] , Shirlee Wohl [aut, ctb] , Justin Lessler [aut, cre]


Documentation:   PDF Manual  


GPL-2 license


Imports reshape2, ggplot2, cowplot, RColorBrewer

Depends on stats

Suggests knitr, rmarkdown, testthat


See at CRAN