Package: bumblebee 0.1.0
bumblebee: Quantify Disease Transmission Within and Between Population Groups
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/>.
Authors:
bumblebee_0.1.0.tar.gz
bumblebee_0.1.0.zip(r-4.5)bumblebee_0.1.0.zip(r-4.4)bumblebee_0.1.0.zip(r-4.3)
bumblebee_0.1.0.tgz(r-4.4-any)bumblebee_0.1.0.tgz(r-4.3-any)
bumblebee_0.1.0.tar.gz(r-4.5-noble)bumblebee_0.1.0.tar.gz(r-4.4-noble)
bumblebee_0.1.0.tgz(r-4.4-emscripten)bumblebee_0.1.0.tgz(r-4.3-emscripten)
bumblebee.pdf |bumblebee.html✨
bumblebee/json (API)
NEWS
| # Install 'bumblebee' in R: |
| install.packages('bumblebee', repos = c('https://magosil86.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/magosil86/bumblebee/issues
- counts_hiv_transmission_pairs - Observed HIV transmission pairs
- estimated_hiv_transmission_flows - Estimated HIV transmission flows
- sampling_frequency - Sampling fequency
epidemiologygeneticsheterogeneityphylogeneticstransmission
Last updated 3 years agofrom:e44b55de83. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 04 2024 |
| R-4.5-win | NOTE | Sep 04 2024 |
| R-4.5-linux | NOTE | Sep 04 2024 |
| R-4.4-win | NOTE | Sep 04 2024 |
| R-4.4-mac | NOTE | Sep 04 2024 |
| R-4.3-win | NOTE | Sep 04 2024 |
| R-4.3-mac | NOTE | Sep 04 2024 |
Exports:estimate_c_hatestimate_multinom_ciestimate_p_hatestimate_prob_group_pairing_and_linkedestimate_theta_hatestimate_transmission_flows_and_ciprep_p_hat
Dependencies:backportsbase64encbslibcachemcheckmatecliclustercolorspacedata.tabledigestdplyrevaluatefansifarverfastmapfontawesomeforeignFormulafsgenericsggplot2gluegridExtragtablegtoolshighrHmischtmlTablehtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmennetpillarpkgconfigR6rappdirsRColorBrewerrlangrmarkdownrpartrstudioapisassscalesstringistringrtibbletidyselecttinytexutf8vctrsviridisviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Observed HIV transmission pairs | counts_hiv_transmission_pairs |
| 'estimate_c_hat' Estimates probability of clustering | c_hat estimate_c_hat estimate_c_hat.default estim_c_hat est_c_hat |
| 'estimate_multinom_ci' Estimates confidence intervals for transmission flows | estimate_multinom_ci estimate_multinom_ci.default estim_multinom_ci est_multinom_ci |
| 'estimate_p_hat' Estimates probability of linkage between two individuals | estimate_p_hat estimate_p_hat.default estim_p_hat est_p_hat phat p_hat |
| 'estimate_prob_group_pairing_and_linked' Estimates joint probability of linkage | estimate_prob_group_pairing_and_linked estimate_prob_group_pairing_and_linked.default prob_group_pairing_and_linked |
| 'estimate_theta_hat' Estimates conditional probability of linkage (transmission flows) | estimate_theta_hat estimate_theta_hat.default estim_theta_hat est_theta_hat theta_hat |
| 'estimate_transmission_flows_and_ci' Estimates transmission flows and corresponding confidence intervals | estimate_transmission_flows_and_ci estimate_transmission_flows_and_ci.default flows_and_ci |
| Estimated HIV transmission flows | estimated_hiv_transmission_flows |
| 'prep_p_hat' Prepares input data to estimate 'p_hat' | pp prep_phat prep_p_hat prep_p_hat.default |
| Sampling fequency | sampling_frequency |
