Description Usage Format Source References
Estimated HIV transmissions within and betweeen intervention and control communities in the BCPP/Ya Tsie trial population adjusted for variability in sampling.
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A data frame:
Name of population group 1
Name of population group 2
Number of individuals sampled from population group 1
Number of individuals sampled from population group 2
Estimated number of individuals in population group 1
Estimated number of individuals in population group 2
Number of distinct possible transmission pairs between individuals sampled from population groups 1 and 2
Number of distinct possible transmission pairs between individuals in population groups 1 and 2
Number of observed directed transmission pairs between samples from population groups 1 and 2
Probability that pathogen sequences from two individuals randomly sampled from their respective population groups are linked
Estimated transmission pairs between population groups 1 and 2
Estimated transmission flows or relative probability of transmission within and between population groups 1 and 2 adjusted for sampling heterogeneity. More precisely, the conditional probability that a pair of pathogen sequences is from a specific population group pairing given that the pair is linked.
Point estimate, Goodman method Confidence intervals for observed transmission pairs
Lower bound of Goodman confidence interval
Upper bound of Goodman confidence interval
Point estimate, Goodman method Confidence intervals for estimated transmission flows
Lower bound of Goodman confidence interval
Upper bound of Goodman confidence interval
Probability that a pair of pathogen sequences is from a specific population group pairing and is linked
Probability that a randomly selected pathogen sequence in one population group links to at least one pathogen sequence in another population group i.e. probability of clustering
Point estimate, Goodman method Confidence intervals with continuity correction
Lower bound of Goodman confidence interval
Upper bound of Goodman confidence interval
Point estimate, Sison-Glaz method Confidence intervals
Lower bound of Sison-Glaz confidence interval
Upper bound of Sison-Glaz confidence interval
Point estimate, Queensbury-Hurst method Confidence intervals via ACSWR r package
Lower bound of Queensbury-Hurst confidence interval
Upper bound of Queensbury-Hurst confidence interval
Point estimate, Queensbury-Hurst method Confidence intervals via CoinMinD r package
Lower bound of Queensbury-Hurst confidence interval
Upper bound of Queensbury-Hurst confidence interval
Lower bound of Queensbury-Hurst confidence interval adjusted
Upper bound of Queensbury-Hurst confidence interval adjusted
https://magosil86.github.io/bumblebee/
Magosi LE, et al., Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/ Ya Tsie trial. To submit for publication, 2021.
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