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 13 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-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 (4 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.
Check History
NOTE 9 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 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.
ERROR 9 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 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.
NOTE 10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 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.
Dependency Network
Version History
1 trackedR Observatory began tracking this package on Mar 10, 2026; it first appeared on CRAN May 11, 2021. Releases before tracking aren’t shown.