Description Usage Arguments Details Value Methods (by class) References See Also Examples
View source: R/driver_estimate_transmissision_flows.r
This function computes the joint probability that a pair of pathogen sequences is from a specific population group pairing and linked.
1 2 3 4 5 6 7 8 9 10 11 12 13 | estimate_prob_group_pairing_and_linked(
df_counts_and_p_hat,
individuals_population_in,
...
)
## Default S3 method:
estimate_prob_group_pairing_and_linked(
df_counts_and_p_hat,
individuals_population_in,
verbose_output = FALSE,
...
)
|
df_counts_and_p_hat |
A data.frame returned by function: |
individuals_population_in |
A numeric vector of the estimated number of individuals per population group |
... |
Further arguments. |
verbose_output |
A boolean value to display intermediate output.
(Default is |
For a population group pairing (u,v), the joint probability that a pair is from groups (u,v) and is linked is computed as
(N_uv / N_choose_2) * p_hat_uv ,
where,
N_uv = N_u * N_v: maximum distinct possible (u,v) pairs in population
p_hat_uv: probability of linkage between two individuals randomly sampled from groups u and v
N choose 2 or (N * (N - 1))/2 : all distinct possible pairs in population.
See bumblebee website for more details https://magosil86.github.io/bumblebee/.
Returns a data.frame containing:
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
prob_group_pairing_and_linked, Probability that a pair of pathogen sequences is from a specific population group pairing and is linked
default
: Estimates joint probability of linkage
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.
Carnegie, N.B., et al., Linkage of viral sequences among HIV-infected village residents in Botswana: estimation of linkage rates in the presence of missing data. PLoS Computational Biology, 2014. 10(1): p. e1003430.
See estimate_p_hat
to prepare input data to estimate prob_group_pairing_and_linked
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | library(bumblebee)
library(dplyr)
# Estimate joint probability that a pair is from a specific group pairing and linked
# We shall use the data of HIV transmissions within and between intervention and control
# communities in the BCPP/Ya Tsie HIV prevention trial. To learn more about the data
# ?counts_hiv_transmission_pairs and ?sampling_frequency
# Load and view data
#
# The input data comprises counts of observed directed HIV transmission pairs
# within and between intervention and control communities in the BCPP/Ya Tsie
# trial, sampling information and the probability of linkage between individuals
# sampled from intervention and control communities (i.e. \code{p_hat})
#
# See ?estimate_p_hat() for details on estimating p_hat
results_estimate_p_hat <- estimated_hiv_transmission_flows[, c(1:10)]
results_estimate_p_hat
# Estimate prob_group_pairing_and_linked
results_prob_group_pairing_and_linked <- estimate_prob_group_pairing_and_linked(
df_counts_and_p_hat = results_estimate_p_hat,
individuals_population_in = sampling_frequency$number_population)
# View results
results_prob_group_pairing_and_linked
|
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