Preliminaries | Data | Filtering | Taxonomic table | Taxonomic tree | References
Package: yatah 1.0.0
Antoine Bichat
yatah: Yet Another TAxonomy Handler
Provides functions to manage taxonomy when lineages are described with strings and ranks separated with special patterns like "|*__" or ";*__".
Authors:
yatah_1.0.0.tar.gz
yatah_1.0.0.zip(r-4.7)yatah_1.0.0.zip(r-4.6)yatah_1.0.0.zip(r-4.5)
yatah_1.0.0.tgz(r-4.6-any)yatah_1.0.0.tgz(r-4.5-any)
yatah_1.0.0.tar.gz(r-4.7-any)yatah_1.0.0.tar.gz(r-4.6-any)
yatah_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
yatah/json (API)
| # Install 'yatah' in R: |
| install.packages('yatah', repos = c('https://abichat.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/abichat/yatah/issues
Pkgdown/docs site:https://abichat.github.io
Datasets:
- abundances - Abundance table for 199 samples.
- all_ranks - Ranks handled by 'yatah'
Last updated from:d5476361fb. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 134 | ||
| source / vignettes | OK | 168 | ||
| linux-release-x86_64 | OK | 124 | ||
| macos-release-arm64 | OK | 94 | ||
| macos-oldrel-arm64 | OK | 98 | ||
| windows-devel | OK | 89 | ||
| windows-release | OK | 79 | ||
| windows-oldrel | OK | 85 | ||
| wasm-release | OK | 111 |
Exports:all_cladesget_all_cladesget_cladeget_last_cladeget_last_rankis_at_least_rankis_cladeis_lineageis_ranklast_cladelast_ranktaxtabletaxtreetrim_commontrim_ranktrim_void
Dependencies:apeclidigestgluelatticelifecyclemagrittrnlmepurrrRcpprlangstringistringrvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Abundance table for 199 samples. | abundances |
| Ranks handled by 'yatah' | all_ranks |
| Extract all clades present in the lineages | get_all_clades |
| Extract the clade of a desired rank in a lineage | get_clade |
| Extract the last clade of a lineage | get_last_clade |
| Extract the last rank of a lineage | get_last_rank |
| Test if a lineage belongs to a clade | is_clade |
| Test if a string is a lineage | is_lineage |
| Test if a lineage goes down to a specified rank | is_at_least_rank is_rank |
| Taxonomic table | taxtable |
| Taxonomic tree | taxtree |
| Trim lineages until the shallowest common rank. | trim_common |
| Trim lineages until a specified rank | trim_rank |
| Trim void ranks in lineages | trim_void |