estimated_hiv_transmission_flows: Estimated HIV transmission flows

Description Usage Format Source References

Description

Estimated HIV transmissions within and betweeen intervention and control communities in the BCPP/Ya Tsie trial population adjusted for variability in sampling.

Usage

1

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.


bumblebee documentation built on May 11, 2021, 5:06 p.m.