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-4.5)yatah_1.0.0.zip(r-4.4)yatah_1.0.0.zip(r-4.3)
yatah_1.0.0.tgz(r-4.4-any)yatah_1.0.0.tgz(r-4.3-any)
yatah_1.0.0.tar.gz(r-4.5-noble)yatah_1.0.0.tar.gz(r-4.4-noble)
yatah_1.0.0.tgz(r-4.4-emscripten)yatah_1.0.0.tgz(r-4.3-emscripten)
yatah.pdf |yatah.html✨
yatah/json (API)
NEWS
| # 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
- abundances - Abundance table for 199 samples.
- all_ranks - Ranks handled by 'yatah'
Last updated 7 months agofrom:d5476361fb. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 09 2024 |
| R-4.5-win | OK | Nov 09 2024 |
| R-4.5-linux | OK | Nov 09 2024 |
| R-4.4-win | OK | Nov 09 2024 |
| R-4.4-mac | OK | Nov 09 2024 |
| R-4.3-win | OK | Nov 09 2024 |
| R-4.3-mac | OK | Nov 09 2024 |
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 |