| estimated_hiv_transmission_flows {bumblebee} | R Documentation |
Estimated HIV transmission flows
Description
Estimated HIV transmissions within and betweeen intervention and control communities in the BCPP/Ya Tsie trial population adjusted for variability in sampling.
Usage
estimated_hiv_transmission_flows
Format
A data frame:
- H1_group
Name of population group 1
- H2_group
Name of population group 2
- number_hosts_sampled_group_1
Number of individuals sampled from population group 1
- number_hosts_sampled_group_2
Number of individuals sampled from population group 2
- number_hosts_population_group_1
Estimated number of individuals in population group 1
- number_hosts_population_group_2
Estimated number of individuals in population group 2
- max_possible_pairs_in_sample
Number of distinct possible transmission pairs between individuals sampled from population groups 1 and 2
- max_possible_pairs_in_population
Number of distinct possible transmission pairs between individuals in population groups 1 and 2
- num_linked_pairs_observed
Number of observed directed transmission pairs between samples from population groups 1 and 2
- p_hat
Probability that pathogen sequences from two individuals randomly sampled from their respective population groups are linked
- est_linkedpairs_in_population
Estimated transmission pairs between population groups 1 and 2
- theta_hat
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.
- obs_trm_pairs_est_goodman
Point estimate, Goodman method Confidence intervals for observed transmission pairs
- obs_trm_pairs_lwr_ci_goodman
Lower bound of Goodman confidence interval
- obs_trm_pairs_upr_ci_goodman
Upper bound of Goodman confidence interval
- est_goodman
Point estimate, Goodman method Confidence intervals for estimated transmission flows
- lwr_ci_goodman
Lower bound of Goodman confidence interval
- upr_ci_goodman
Upper bound of Goodman confidence interval
- prob_group_pairing_and_linked
Probability that a pair of pathogen sequences is from a specific population group pairing and is linked
- c_hat
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
- est_goodman_cc
Point estimate, Goodman method Confidence intervals with continuity correction
- lwr_ci_goodman_cc
Lower bound of Goodman confidence interval
- upr_ci_goodman_cc
Upper bound of Goodman confidence interval
- est_sisonglaz
Point estimate, Sison-Glaz method Confidence intervals
- lwr_ci_sisonglaz
Lower bound of Sison-Glaz confidence interval
- upr_ci_sisonglaz
Upper bound of Sison-Glaz confidence interval
- est_qhurst_acswr
Point estimate, Queensbury-Hurst method Confidence intervals via ACSWR r package
- lwr_ci_qhurst_acswr
Lower bound of Queensbury-Hurst confidence interval
- upr_ci_qhurst_acswr
Upper bound of Queensbury-Hurst confidence interval
- est_qhurst_coinmind
Point estimate, Queensbury-Hurst method Confidence intervals via CoinMinD r package
- lwr_ci_qhurst_coinmind
Lower bound of Queensbury-Hurst confidence interval
- upr_ci_qhurst_coinmind
Upper bound of Queensbury-Hurst confidence interval
- lwr_ci_qhurst_adj_coinmind
Lower bound of Queensbury-Hurst confidence interval adjusted
- upr_ci_qhurst_adj_coinmind
Upper bound of Queensbury-Hurst confidence interval adjusted
Source
https://magosil86.github.io/bumblebee/
References
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.