bumblebee
Quantify Disease Transmission Within and Between Population Groups
Description
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/>.
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CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | NOTE |
| r-devel-linux-x86_64-debian-gcc | NOTE |
| r-devel-linux-x86_64-fedora-clang | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (14 non-OK)
CRAN incoming feasibility
Maintainer: ‘Lerato E Magosi <magosil86@gmail.com>’ Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead.
CRAN incoming feasibility
Maintainer: ‘Lerato E Magosi <magosil86@gmail.com>’ Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead.
dependencies in R code
Namespaces in Imports field not imported from: ‘Hmisc’ ‘magrittr’ ‘rmarkdown’ All declared Imports should be used.
dependencies in R code
Namespaces in Imports field not imported from: ‘Hmisc’ ‘magrittr’ ‘rmarkdown’ All declared Imports should be used.
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Check History
NOTE 10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026
CRAN incoming feasibility
Maintainer: ‘Lerato E Magosi <magosil86@gmail.com>’ Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead.
CRAN incoming feasibility
Maintainer: ‘Lerato E Magosi <magosil86@gmail.com>’ Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead.
dependencies in R code
Namespaces in Imports field not imported from: ‘Hmisc’ ‘magrittr’ ‘rmarkdown’ All declared Imports should be used.
dependencies in R code
Namespaces in Imports field not imported from: ‘Hmisc’ ‘magrittr’ ‘rmarkdown’ All declared Imports should be used.