Quantify Disease Transmission Within and Between Population Groups
Bumblebee: Quantify Disease Transmission Within and Between Population...
estimate_c_hat Estimates probability of clustering
estimate_multinom_ci Estimates confidence intervals for transmission...
estimate_p_hat Estimates probability of linkage between two individu...
estimate_prob_group_pairing_and_linked Estimates joint probability o...
estimate_theta_hat Estimates conditional probability of linkage (tra...
estimate_transmission_flows_and_ci Estimates transmission flows and ...
prep_p_hat Prepares input data to estimate p_hat
A simple tool to quantify the amount of transmission of an infectious disease of interest occurring within and between population groups. 'bumblebee' uses counts of observed directed transmission pairs, identified phylogenetically from deep-sequence data or from epidemiological contacts, to quantify transmission flows within and between population groups accounting for sampling heterogeneity. Population groups might include: geographical areas (e.g. communities, regions), demographic groups (e.g. age, gender) or arms of a randomized clinical trial. See the 'bumblebee' website for statistical theory, documentation and examples <https://magosil86.github.io/bumblebee/>.