Installation | Transmission assortativity | Gamma | Delta | Estimation | Example | Data | Visualise the transmission tree | Estimate the transmission assortativity coefficient
Package: linktree 0.1.0
linktree: Estimate Transmission Assortativity Coefficients
Estimates group transmission assortativity coefficients from transmission trees. Group transmission assortativity coefficients measure the tendency for individuals to transmit within their own group (e.g. age group, vaccination status, or location) compared to other groups. The package requires information on who infected whom, group membership for all individuals, and the relative sizes of each group in the population. For more details see Geismar et al. (2024) <doi:10.1371/journal.pone.0313037>.
Authors:
linktree_0.1.0.tar.gz
linktree_0.1.0.zip(r-4.7)linktree_0.1.0.zip(r-4.6)linktree_0.1.0.zip(r-4.5)
linktree_0.1.0.tgz(r-4.6-any)linktree_0.1.0.tgz(r-4.5-any)
linktree_0.1.0.tar.gz(r-4.7-any)linktree_0.1.0.tar.gz(r-4.6-any)
linktree_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
linktree/json (API)
| # Install 'linktree' in R: |
| install.packages('linktree', repos = c('https://cygei.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cygei/linktree/issues
Pkgdown/docs site:https://cygei.github.io
Datasets:
- sim_tree - Simulated transmission tree
Last updated from:288487bce0. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 174 | ||
| source / vignettes | OK | 205 | ||
| linux-release-x86_64 | OK | 145 | ||
| macos-release-arm64 | OK | 114 | ||
| macos-oldrel-arm64 | OK | 118 | ||
| windows-devel | OK | 78 | ||
| windows-release | OK | 80 | ||
| windows-oldrel | OK | 96 | ||
| wasm-release | OK | 100 |
Exports:delta2gammagamma2deltaget_deltaget_gammaget_pi
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert delta to gamma | delta2gamma |
| Convert gamma to delta | gamma2delta |
| Calculate delta | get_delta |
| Calculate gamma | get_gamma |
| Calculate Pi Values | get_pi |
| Plot linktree objects | plot.linktree |
| Simulated transmission tree | sim_tree |
